diff --git a/.gitignore b/.gitignore index 1f57ac3..a708088 100644 --- a/.gitignore +++ b/.gitignore @@ -56,3 +56,4 @@ __pycache__/ # and can be added to the global gitignore or merged into this file. For a more nuclear # option (not recommended) you can uncomment the following to ignore the entire idea folder. #.idea/ +tests/qualimap_ref/ diff --git a/README.md b/README.md index 35b6000..cbad7c1 100644 --- a/README.md +++ b/README.md @@ -62,9 +62,9 @@ All RSeQC tools run by default when annotation is provided via `--gtf` or `--bed | Tool | Upstream equivalent | Description | |------|-------------------|-------------| +| Qualimap rnaseq | [Qualimap](http://qualimap.conesalab.org/) rnaseq | Full RNA-Seq QC: gene body coverage profiling (5'→3'), 5'/3' bias metrics, read origin classification (exonic/intronic/intergenic), strand-specificity estimation, and junction analysis. Qualimap-compatible output parseable by MultiQC. | | preseq | [`preseq lc_extrap`](http://smithlabresearch.org/software/preseq/) | Library complexity extrapolation -- estimates distinct molecules at increasing sequencing depths | | TIN | [`tin.py`](https://rseqc.sourceforge.net/#tin-py) | Transcript Integrity Number -- measures transcript degradation via coverage uniformity | -| Gene body coverage | [Qualimap](http://qualimap.conesalab.org/) rnaseq | Coverage profile along gene bodies (5'→3'), Qualimap-compatible output for MultiQC | | flagstat | [`samtools flagstat`](http://www.htslib.org/) | Alignment flag summary statistics, identical format to samtools | | idxstats | [`samtools idxstats`](http://www.htslib.org/) | Per-chromosome read counts, identical format to samtools | | stats | [`samtools stats`](http://www.htslib.org/) | Summary Numbers (SN) section, MultiQC-compatible format | @@ -358,12 +358,16 @@ RSeQC outputs are organized into per-tool subdirectories under `rseqc/`. | `samtools/sample.idxstats` | samtools idxstats-compatible per-chromosome read counts | | `samtools/sample.stats` | samtools stats SN-section compatible summary numbers (MultiQC-parseable) | -### Gene body coverage outputs (`qualimap/`) +### Qualimap outputs (`qualimap/`) + +Reimplements [Qualimap](http://qualimap.conesalab.org/) rnaseq mode. The output files are written in the same format and directory structure as Qualimap, making them directly parseable by [MultiQC](https://multiqc.info/). Qualimap analyses only run in GTF mode (skipped with `--bed`). | File | Description | |------|-------------| -| `qualimap/coverage_profile_along_genes_(total).txt` | Gene body coverage profile (100 percentile bins, 5'→3') | -| `qualimap/rnaseq_qc_results.txt` | Qualimap rnaseq-compatible QC results (MultiQC-parseable) | +| `qualimap/rnaseq_qc_results.txt` | Qualimap rnaseq-compatible QC report: alignment statistics, read origin (exonic/intronic/intergenic/overlapping exon), 5'/3' coverage bias, strand specificity, and junction analysis. MultiQC-parseable. | +| `qualimap/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt` | Gene body coverage profile across all genes (100 percentile bins, 5'→3') | +| `qualimap/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt` | Gene body coverage profile for highly-expressed genes (top 500 by mean coverage) | +| `qualimap/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt` | Gene body coverage profile for lowly-expressed genes (bottom 500 by mean coverage) | ### Duplication matrix columns @@ -418,16 +422,18 @@ Note: PGO profiles are machine-specific and `target-cpu=native` produces non-por ### `rustqc rna` -1. **GTF parsing**: Reads gene annotations (plain or gzip-compressed), computes effective gene lengths from non-overlapping exon bases, and extracts additional attributes (e.g., biotype) for downstream grouping. +1. **GTF parsing**: Reads gene annotations (plain or gzip-compressed), computes effective gene lengths from non-overlapping exon bases, and extracts additional attributes (e.g., biotype) for downstream grouping. Builds interval trees for merged exon regions used by the Qualimap module. 2. **Read counting**: Reads the alignment file (SAM/BAM/CRAM) once, assigning each read to a gene based on exon overlap. Four count modes are tracked simultaneously: - With/without multimappers x with/without duplicates - Assignment statistics (assigned, ambiguous, no features) are tracked for the featureCounts summary. + - Qualimap accumulator runs in the same pass: per-transcript coverage, gene body profiling, read origin classification (exonic/intronic/intergenic), overlapping-exon detection, strand-specificity estimation, and splice junction motif counting. 3. **featureCounts output**: Writes gene-level counts and summary statistics in the standard featureCounts format. 4. **Biotype counting**: Aggregates assigned read counts by a configurable GTF attribute (e.g., `gene_biotype`), producing biotype count tables and MultiQC-compatible rRNA QC metrics. 5. **Duplication matrix**: Computes RPK, RPKM, and duplication rates for each gene in all four modes. 6. **Logistic regression**: Fits a binomial GLM (`dupRate ~ log10(RPK)`) using iteratively reweighted least squares (IRLS) to model the relationship between expression and duplication. -7. **Plots**: Generates density scatter, boxplot, and histogram visualizations. -8. **MultiQC integration**: Outputs files compatible with [MultiQC](https://multiqc.info/) for pipeline reporting (dupRadar intercept, fit curve, biotype bargraph, rRNA percentage). +7. **Qualimap output**: Computes gene body coverage profiles (total, high-expression, low-expression tiers), 5'/3' bias metrics, and produces a Qualimap-compatible `rnaseq_qc_results.txt` report with read origin counts, mapping statistics, and strand specificity. +8. **Plots**: Generates density scatter, boxplot, and histogram visualizations. +9. **MultiQC integration**: Outputs files compatible with [MultiQC](https://multiqc.info/) for pipeline reporting (dupRadar intercept, fit curve, biotype bargraph, rRNA percentage, Qualimap rnaseq reports). ### RSeQC tools @@ -454,6 +460,8 @@ Each RSeQC tool is a single-pass BAM reader that processes the alignment file an - Original dupRadar R package: https://github.com/ssayols/dupRadar - Wang L, Wang S, Li W (2012). RSeQC: quality control of RNA-seq experiments. *Bioinformatics*, 28(16), 2184-2185. doi:10.1093/bioinformatics/bts356 - RSeQC: https://rseqc.sourceforge.net/ +- García-Alcalde F, Okonechnikov K, Carbonell J, et al. (2012). Qualimap: evaluating next-generation sequencing alignment data. *Bioinformatics*, 28(20), 2678-2679. doi:10.1093/bioinformatics/bts503 +- Qualimap: http://qualimap.conesalab.org/ ## License diff --git a/benchmark/README.md b/benchmark/README.md index f96d368..09cbec0 100644 --- a/benchmark/README.md +++ b/benchmark/README.md @@ -355,32 +355,57 @@ docker run --rm --platform linux/amd64 \ ### 9. Generate Qualimap reference outputs -Reference outputs for validating the gene body coverage reimplementation are -stored in `qualimap/small/` and `qualimap/large/`. These were generated with +Reference outputs for validating the Qualimap reimplementation are stored in +`qualimap/small/` and `qualimap/large/`. These were generated with [Qualimap 2.3](http://qualimap.conesalab.org/) run via Docker. +> **Note:** Qualimap Java requires a **name-sorted BAM** (`samtools sort -n`). +> The `-p strand-specific-reverse` and `-s` flags match the library preparation +> of the GM12878 dataset. Both tools must use the same GTF and strandedness +> settings for results to be comparable. + ```bash QUALIMAP_IMG="quay.io/biocontainers/qualimap:2.3--hdfd78af_0" -# Small (requires uncompressed GTF) +# Small (name-sort BAM first, requires uncompressed GTF) gunzip -k benchmark/input/small/chr6.gtf.gz +samtools sort -n -o benchmark/input/small/test.namesorted.bam benchmark/input/small/test.bam docker run --rm -v $(pwd)/benchmark:/data \ $QUALIMAP_IMG qualimap rnaseq \ - -bam /data/input/small/test.bam -gtf /data/input/small/chr6.gtf \ - -outdir /data/qualimap_tmp_small --java-mem-size=4G -pe + -bam /data/input/small/test.namesorted.bam -gtf /data/input/small/chr6.gtf \ + -outdir /data/qualimap_tmp_small --java-mem-size=4G \ + -p strand-specific-reverse -pe -s cp benchmark/qualimap_tmp_small/rnaseq_qc_results.txt benchmark/qualimap/small/ cp "benchmark/qualimap_tmp_small/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt" benchmark/qualimap/small/ -# Large -gunzip -k benchmark/input/large/genes.gtf.gz +# Large (requires name-sorted BAM and filtered GTF) docker run --rm -v $(pwd)/benchmark:/data \ $QUALIMAP_IMG qualimap rnaseq \ - -bam /data/input/large/GM12878_REP1.markdup.sorted.bam -gtf /data/input/large/genes.gtf \ - -outdir /data/qualimap_tmp_large --java-mem-size=8G -pe + -bam /data/input/large/GM12878_REP1.namesorted.bam \ + -gtf /data/input/large/genes.filtered.gtf \ + -outdir /data/qualimap_tmp_large --java-mem-size=8G \ + -p strand-specific-reverse -pe -s cp benchmark/qualimap_tmp_large/rnaseq_qc_results.txt benchmark/qualimap/large/ cp "benchmark/qualimap_tmp_large/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt" benchmark/qualimap/large/ ``` +To generate matching RustQC Qualimap outputs for comparison, run with the same +strandedness and GTF as the Java reference: + +```bash +# Small (coord-sorted BAM, same GTF and strandedness as Java run) +cargo run --release -- rna benchmark/input/small/test.bam \ + --gtf benchmark/input/small/chr6.gtf \ + --paired --stranded 2 --skip-dup-check \ + --outdir benchmark/RustQC/small + +# Large (coord-sorted BAM, filtered GTF, same strandedness) +cargo run --release -- rna benchmark/input/large/GM12878_REP1.markdup.sorted.bam \ + --gtf benchmark/input/large/genes.filtered.gtf \ + --paired --stranded 2 --biotype-attribute gene_biotype --threads 10 \ + --outdir benchmark/RustQC/large +``` + ### 10. Compare results ```bash diff --git a/benchmark/RustQC/large/dupradar/GM12878_REP1.markdup.sorted_dupMatrix.txt b/benchmark/RustQC/large/dupradar/GM12878_REP1.markdup.sorted_dupMatrix.txt index f568f0a..f39d334 100644 --- a/benchmark/RustQC/large/dupradar/GM12878_REP1.markdup.sorted_dupMatrix.txt +++ b/benchmark/RustQC/large/dupradar/GM12878_REP1.markdup.sorted_dupMatrix.txt @@ -1,185 +1,185 @@ ID geneLength allCountsMulti filteredCountsMulti dupRateMulti dupsPerIdMulti RPKMulti PKMMulti allCounts filteredCounts dupRate dupsPerId RPK RPKM -ENSG00000290825.1 1657 31 15 0.516129032258065 16 18.7085093542547 0.201158617081565 0 0 NA 0 0 0 +ENSG00000290825.1 1657 56 26 0.535714285714286 30 33.7960168980085 0.181974380975024 0 0 NA 0 0 0 ENSG00000223972.6 632 0 0 NA 0 0 0 0 0 NA 0 0 0 -ENSG00000227232.6 1380 4085 2798 0.315055079559364 1287 2960.14492753623 31.8282257933488 685 203 0.703649635036496 482 496.376811594203 5.33716882948444 -ENSG00000278267.1 68 0 0 NA 0 0 0 0 0 NA 0 0 0 -ENSG00000243485.5 1021 1 1 0 0 0.979431929480901 0.010531099444067 0 0 NA 0 0 0 +ENSG00000227232.6 1380 7257 4945 0.31858894860135 2312 5258.69565217391 28.3154044137311 1260 363 0.711904761904762 897 913.04347826087 4.91627525992851 +ENSG00000278267.1 68 31 19 0.387096774193548 12 455.882352941176 2.45469486017439 8 3 0.625 5 117.647058823529 0.633469641335326 +ENSG00000243485.5 1021 2 2 0 0 1.9588638589618 0.010547486682371 0 0 NA 0 0 0 ENSG00000284332.1 138 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000237613.2 1219 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000268020.3 840 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000290826.1 1414 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000240361.3 939 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000186092.7 2618 0 0 NA 0 0 0 0 0 NA 0 0 0 -ENSG00000238009.7 3569 15 15 0 0 4.20285794340151 0.045190189965223 0 0 NA 0 0 0 +ENSG00000238009.7 3569 35 31 0.114285714285714 4 9.80666853460353 0.052803927794133 0 0 NA 0 0 0 ENSG00000239945.1 1319 0 0 NA 0 0 0 0 0 NA 0 0 0 -ENSG00000233750.3 3812 129 124 0.038759689922481 5 33.8405036726128 0.363861641311273 0 0 NA 0 0 0 -ENSG00000268903.1 755 1158 812 0.298791018998273 346 1533.77483443709 16.4915343476953 265 63 0.762264150943396 202 350.993377483444 3.77396943189919 -ENSG00000269981.1 284 606 325 0.463696369636964 281 2133.80281690141 22.9431867416534 327 88 0.730886850152905 239 1151.40845070423 12.3802344299021 -ENSG00000239906.1 323 311 246 0.209003215434084 65 962.848297213622 10.3527880420245 17 7 0.588235294117647 10 52.6315789473684 0.565908028020633 -ENSG00000241860.7 7559 2078 1811 0.128488931665063 267 274.904087842307 2.95583817466737 58 27 0.53448275862069 31 7.67297261542532 0.082501739235182 -ENSG00000222623.1 104 6 3 0.5 3 57.6923076923077 0.620322261484155 1 1 0 0 9.61538461538461 0.103387043580693 -ENSG00000241599.1 457 22 10 0.545454545454545 12 48.1400437636761 0.51761390746745 1 1 0 0 2.18818380743982 0.023527904884884 +ENSG00000233750.3 3812 254 244 0.039370078740157 10 66.6316894018888 0.358777795289342 0 0 NA 0 0 0 +ENSG00000268903.1 755 2005 1460 0.271820448877805 545 2655.62913907285 14.299213725109 415 95 0.771084337349398 320 549.668874172185 2.9596876288879 +ENSG00000269981.1 284 731 383 0.476060191518468 348 2573.94366197183 13.8593789311164 412 115 0.720873786407767 297 1450.70422535211 7.81130522519829 +ENSG00000239906.1 323 474 382 0.194092827004219 92 1467.49226006192 7.90170026297223 17 7 0.588235294117647 10 52.6315789473684 0.283394313228962 +ENSG00000241860.7 7559 3705 3247 0.12361673414305 458 490.144198968117 2.63917749434486 103 48 0.533980582524272 55 13.626141023945 0.073369846671395 +ENSG00000222623.1 104 6 3 0.5 3 57.6923076923077 0.310643766424054 1 1 0 0 9.61538461538461 0.051773961070676 +ENSG00000241599.1 457 31 17 0.451612903225806 14 67.8336980306346 0.365250001076277 2 2 0 0 4.37636761487965 0.023564516198469 ENSG00000279928.2 570 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000279457.4 1397 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000273874.1 68 0 0 NA 0 0 0 0 0 NA 0 0 0 -ENSG00000292994.1 8224 24 22 0.083333333333333 2 2.91828793774319 0.031378168868848 0 0 NA 0 0 0 +ENSG00000292994.1 8224 47 43 0.085106382978723 4 5.71498054474708 0.030772266745314 0 0 NA 0 0 0 ENSG00000228463.11 457 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000286448.1 736 0 0 NA 0 0 0 0 0 NA 0 0 0 -ENSG00000236679.2 385 1 1 0 0 2.5974025974026 0.027927928655564 0 0 NA 0 0 0 -ENSG00000236601.2 1095 3 3 0 0 2.73972602739726 0.029458226116143 0 0 NA 0 0 0 -ENSG00000290385.1 6204 8 8 0 0 1.28949065119278 0.013864929119783 0 0 NA 0 0 0 -ENSG00000269732.1 363 5 3 0.4 2 13.7741046831956 0.148102651961323 0 0 NA 0 0 0 -ENSG00000284733.2 939 9 9 0 0 9.58466453674121 0.103056733537304 0 0 NA 0 0 0 +ENSG00000236679.2 385 2 2 0 0 5.19480519480519 0.027971386760261 0 0 NA 0 0 0 +ENSG00000236601.2 1095 3 3 0 0 2.73972602739726 0.014752032743425 0 0 NA 0 0 0 +ENSG00000290385.1 6204 8 8 0 0 1.28949065119278 0.006943252032689 0 0 NA 0 0 0 +ENSG00000269732.1 363 7 5 0.285714285714286 2 19.2837465564738 0.103833178125212 0 0 NA 0 0 0 +ENSG00000284733.2 939 18 18 0 0 19.1693290734824 0.103217098108951 0 0 NA 0 0 0 ENSG00000237094.13 183 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000233653.3 2477 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000250575.1 1239 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000278757.1 104 0 0 NA 0 0 0 0 0 NA 0 0 0 -ENSG00000293331.1 5481 58 25 0.568965517241379 33 10.5820105820106 0.113780450078222 39 8 0.794871794871795 31 7.11548987411056 0.076507544018115 -ENSG00000235146.2 635 1 1 0 0 1.5748031496063 0.016932681153373 0 0 NA 0 0 0 -ENSG00000225972.1 372 1 1 0 0 2.68817204301075 0.028903904656968 0 0 NA 0 0 0 -ENSG00000225630.1 1044 3 3 0 0 2.8735632183908 0.030897277391931 0 0 NA 0 0 0 -ENSG00000237973.1 1543 1 1 0 0 0.648088139987038 0.006968407344389 0 0 NA 0 0 0 +ENSG00000293331.1 5481 88 34 0.613636363636364 54 16.0554643313264 0.086450518467218 65 13 0.8 52 11.8591497901843 0.063855496595105 +ENSG00000235146.2 635 2 2 0 0 3.1496062992126 0.016959029768032 0 0 NA 0 0 0 +ENSG00000225972.1 372 1 1 0 0 2.68817204301075 0.014474440729436 0 0 NA 0 0 0 +ENSG00000225630.1 1044 6 6 0 0 5.74712643678161 0.030945356042243 0 0 NA 0 0 0 +ENSG00000237973.1 1543 2 2 0 0 1.29617627997408 0.006979250747052 0 0 NA 0 0 0 ENSG00000278791.1 89 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000229344.1 682 0 0 NA 0 0 0 0 0 NA 0 0 0 -ENSG00000240409.1 207 1 1 0 0 4.83091787439614 0.051943248948754 0 0 NA 0 0 0 -ENSG00000248527.1 681 8 8 0 0 11.7474302496329 0.126311336650714 0 0 NA 0 0 0 +ENSG00000240409.1 207 1 1 0 0 4.83091787439614 0.02601203841232 0 0 NA 0 0 0 +ENSG00000248527.1 681 16 16 0 0 23.4948604992658 0.126507887256394 0 0 NA 0 0 0 ENSG00000198744.5 547 0 0 NA 0 0 0 0 0 NA 0 0 0 -ENSG00000268663.1 424 541 483 0.10720887245841 58 1275.94339622642 13.7192656132643 31 8 0.741935483870968 23 73.1132075471698 0.78613167100036 -ENSG00000284662.2 939 86 78 0.093023255813953 8 91.5867944621938 0.984764342689791 9 2 0.777777777777778 7 9.58466453674121 0.103056733537304 +ENSG00000268663.1 424 627 549 0.124401913875598 78 1478.77358490566 7.96244446579392 38 10 0.736842105263158 28 89.622641509434 0.482572391866298 +ENSG00000284662.2 939 170 155 0.088235294117647 15 181.043663471778 0.974828148806759 16 3 0.8125 13 17.0394036208733 0.091748531652401 ENSG00000230021.11 183 0 0 NA 0 0 0 0 0 NA 0 0 0 -ENSG00000229376.3 2455 98 60 0.387755102040816 38 39.918533604888 0.429214154042533 50 16 0.68 34 20.3665987780041 0.218986813287007 -ENSG00000291215.1 7026 380 127 0.66578947368421 253 54.0848277825221 0.581533726488609 325 99 0.695384615384615 226 46.2567606034728 0.497364371338942 -ENSG00000223181.1 104 18 15 0.166666666666667 3 173.076923076923 1.86096678445247 7 4 0.428571428571429 3 67.3076923076923 0.723709305064848 -ENSG00000229905.1 456 24 11 0.541666666666667 13 52.6315789473684 0.565908028020633 20 7 0.65 13 43.859649122807 0.471590023350527 +ENSG00000229376.3 2455 179 114 0.363128491620112 65 72.9124236252546 0.392596358163625 84 27 0.678571428571429 57 34.2158859470468 0.184235162490193 +ENSG00000291215.1 7026 636 213 0.665094339622642 423 90.5209222886422 0.487409177491998 554 168 0.696750902527076 386 78.8499857671506 0.424567113727306 +ENSG00000223181.1 104 18 15 0.166666666666667 3 173.076923076923 0.931931299272163 7 4 0.428571428571429 3 67.3076923076923 0.36241772749473 +ENSG00000229905.1 456 29 12 0.586206896551724 17 63.5964912280702 0.342434795151662 25 8 0.68 17 54.8245614035088 0.295202409613502 ENSG00000228327.6 417 0 0 NA 0 0 0 0 0 NA 0 0 0 -ENSG00000237491.10 8413 364 127 0.651098901098901 237 43.2663734696303 0.465210973706252 251 80 0.681274900398406 171 29.8347795079044 0.320791083517223 +ENSG00000237491.10 8413 571 195 0.658493870402802 376 67.8711517888981 0.365451670536195 396 125 0.684343434343434 271 47.0700106977297 0.253448093751897 ENSG00000285268.1 114 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000290784.1 872 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000230092.8 238 0 0 NA 0 0 0 0 0 NA 0 0 0 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ENSG00000215537.3 1213 0 0 NA 0 0 0 0 0 NA 0 0 0 -ENSG00000226906.1 1346 3 3 0 0 2.22882615156018 0.023964901632374 0 0 NA 0 0 0 -ENSG00000183753.10 1436 1 1 0 0 0.696378830083565 0.00748764103927 0 0 NA 0 0 0 +ENSG00000226906.1 1346 3 3 0 0 2.22882615156018 0.012001096474035 0 0 NA 0 0 0 +ENSG00000183753.10 1436 2 2 0 0 1.39275766016713 0.007499292411351 0 0 NA 0 0 0 ENSG00000244000.1 759 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000232764.1 762 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000233126.3 1465 0 0 NA 0 0 0 0 0 NA 0 0 0 @@ -63032,7 +63032,7 @@ ENSG00000252948.1 104 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000233843.1 323 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000188399.5 659 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000277146.1 111 0 0 NA 0 0 0 0 0 NA 0 0 0 -ENSG00000215506.5 1605 32 32 0 0 19.9376947040498 0.214375128371679 0 0 NA 0 0 0 +ENSG00000215506.5 1605 38 38 0 0 23.6760124610592 0.127483298536642 0 0 NA 0 0 0 ENSG00000224240.1 319 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000227629.1 342 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000237917.1 2337 0 0 NA 0 0 0 0 0 NA 0 0 0 diff --git a/benchmark/RustQC/large/dupradar/GM12878_REP1.markdup.sorted_dup_intercept_mqc.txt b/benchmark/RustQC/large/dupradar/GM12878_REP1.markdup.sorted_dup_intercept_mqc.txt index 8017fe8..2bc8edb 100644 --- a/benchmark/RustQC/large/dupradar/GM12878_REP1.markdup.sorted_dup_intercept_mqc.txt +++ b/benchmark/RustQC/large/dupradar/GM12878_REP1.markdup.sorted_dup_intercept_mqc.txt @@ -9,4 +9,4 @@ # min: 0 # format: '{:.2f}' Sample dupRadar_intercept -GM12878_REP1.markdup.sorted 0.8245216334168248 +GM12878_REP1.markdup.sorted 0.7419969763829039 diff --git a/benchmark/RustQC/large/dupradar/GM12878_REP1.markdup.sorted_duprateExpBoxplot.png b/benchmark/RustQC/large/dupradar/GM12878_REP1.markdup.sorted_duprateExpBoxplot.png index 50b4b5f..61a9ad4 100644 Binary files a/benchmark/RustQC/large/dupradar/GM12878_REP1.markdup.sorted_duprateExpBoxplot.png and b/benchmark/RustQC/large/dupradar/GM12878_REP1.markdup.sorted_duprateExpBoxplot.png differ diff --git a/benchmark/RustQC/large/dupradar/GM12878_REP1.markdup.sorted_duprateExpBoxplot.svg b/benchmark/RustQC/large/dupradar/GM12878_REP1.markdup.sorted_duprateExpBoxplot.svg index 13a5678..794e9e8 100644 --- a/benchmark/RustQC/large/dupradar/GM12878_REP1.markdup.sorted_duprateExpBoxplot.svg +++ b/benchmark/RustQC/large/dupradar/GM12878_REP1.markdup.sorted_duprateExpBoxplot.svg @@ -119,25 +119,25 @@ mean expression (reads/kbp) 60 - 65 % / 0.0 -65 - 70 % / 1.6 +65 - 70 % / 2.5 -70 - 75 % / 5.0 +70 - 75 % / 7.6 -75 - 80 % / 11.6 +75 - 80 % / 17.6 -80 - 85 % / 25.1 +80 - 85 % / 37.9 -85 - 90 % / 58.2 +85 - 90 % / 86.0 -90 - 95 % / 158.4 +90 - 95 % / 231.8 -95 - 100 % / 1627.1 +95 - 100 % / 2464.4 @@ -146,19 +146,19 @@ mean expression (reads/kbp) - - - + + + - + - - - + + + - + @@ -405,69 +405,82 @@ mean expression (reads/kbp) - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - 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+1283,14 @@ mean expression (reads/kbp) - - - - - - + + - - - - - - - - - + + @@ -1255,95 +1298,87 @@ mean expression (reads/kbp) - + - - - + + + + + + + - + + + + - - - + + - - - - - + - - - - - - + + + + + - - - + + + + - + - - - - - + + + + + + + - - - - - - - - - - - - - - + + - + + + + - - - @@ -1352,16 +1387,6 @@ mean expression (reads/kbp) - - - - - - - - - - @@ -1372,6 +1397,7 @@ mean expression (reads/kbp) + @@ -1380,20 +1406,14 @@ mean expression (reads/kbp) + - - - - - - - @@ -1404,20 +1424,22 @@ mean expression (reads/kbp) - + + - + - + + @@ -1427,10 +1449,9 @@ mean expression (reads/kbp) - - - + + @@ -1438,31 +1459,31 @@ mean expression (reads/kbp) + + + + - - - - - - - - + + + - - - + + - - + + + - - + + + diff --git a/benchmark/RustQC/large/dupradar/GM12878_REP1.markdup.sorted_duprateExpDens.png b/benchmark/RustQC/large/dupradar/GM12878_REP1.markdup.sorted_duprateExpDens.png index 46897d8..133347e 100644 Binary files a/benchmark/RustQC/large/dupradar/GM12878_REP1.markdup.sorted_duprateExpDens.png and b/benchmark/RustQC/large/dupradar/GM12878_REP1.markdup.sorted_duprateExpDens.png differ diff --git a/benchmark/RustQC/large/dupradar/GM12878_REP1.markdup.sorted_duprateExpDens.svg b/benchmark/RustQC/large/dupradar/GM12878_REP1.markdup.sorted_duprateExpDens.svg index fddf440..2b4a2b1 100644 --- a/benchmark/RustQC/large/dupradar/GM12878_REP1.markdup.sorted_duprateExpDens.svg +++ b/benchmark/RustQC/large/dupradar/GM12878_REP1.markdup.sorted_duprateExpDens.svg @@ -135,9310 +135,9907 @@ expression (reads/kbp) 1e+06 - + - - - - - + + + + + + + - - - - - - - - - - - - - - + + + + + + + + + - - - - + + + + + + + + + + + - - - - - - - + + + + + + - - - - - - - + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - 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45.755730853743835 -1.3254874227693798 46.76317061673733 -1.5875444831493841 47.773256509053944 -1.9014118449440383 48.78516681251813 -2.2773327251412145 49.798073839460976 -2.7275754880719996 50.81114663409733 -3.266834029564073 51.82355369664522 -3.912707319518237 52.83446571123541 -4.686273753017824 53.84305825861323 -5.612779054204293 54.848514494816655 -6.722460183003024 55.850027777419534 -8.051532133303896 56.846804221549554 -9.643369827244712 57.838065168717215 -11.549923677303147 58.82304955250694 -13.833415013768322 59.801016146371225 -16.56836670870832 60.771245680106965 -19.844035266853112 61.73304281306222 -23.767323755885734 62.68573795369324 -28.466270641065595 63.62868891674174 -34.09422838403181 64.56128241100416 -40.83486817643092 65.48293535239246 -48.90817414033238 66.39309599871213 -58.57762261913465 67.29124490428701 -70.15878085868017 68.17689569421405 -84.02960570080273 69.04959565961764 -100.64277839227586 69.90892617677173 -120.54047806176943 70.75450295435198 -144.3720760045612 71.58597611435796 -172.91532823676042 72.40303011339432 -207.10175794855206 73.20538351201205 -248.04705622541886 73.99278860068445 -297.0874931799512 74.76503089171813 -355.82352778957477 75.521928486985 -426.1720396688926 76.26333133180366 -510.42888738642176 76.98912036560348 -611.3438349474097 77.69920658018064 -732.2102917056584 78.39352999640596 -876.9727944108646 79.07205857018262 -1050.3557391214106 79.73478703828567 -1258.017564212388 80.38173571445412 -1506.7354163177781 81.01294924576541 -1804.6263258714148 81.62849533890802 -2161.4121104201345 82.22846346549531 -2588.736650960107 82.81296355504097 -3100.5458957669603 83.3821246836581 -3713.5429933330465 83.9360937659546 -4447.733407900966 84.47503425699162 -5327.077807709176 84.99912487055693 -6380.274033281136 85.50855831938468 -7641.693665681094 86.0035400823433 -9152.503760105748 86.48428720301017 -10962.010353143818 86.95102712346873 -13129.267589729334 87.40399655660141 -15725.004984444415 87.84344039961383 -18833.93571429965 88.26961069101816 -22557.521275272597 88.68276561282538 -27017.282728539863 89.08316853924929 -32358.766600566265 89.47108713281497 -38756.29486616823 89.84679248838452 -46418.65403260144 90.21055832526854 -55595.90899075455 90.56266022728178 -66587.56400686255 90.90337493032263 -79752.33719274902 91.23297965680976 -95519.8674492793 91.55175149609376 -114404.735944935 91.85996682977465 -137023.2597274101 92.15790080069704 -164113.60553606908 92.44582682426052 -196559.88023952083 92.72401614057439 +0.0028738605143060775 16.398453638470375 +0.00344656386698453 16.972733806742948 +0.004133395629353153 17.562900488307424 +0.004957099327947097 18.169097465018734 +0.005944950822667564 18.79144833922408 +0.007129661510852212 19.430055090252964 +0.008550461521987584 20.084996632833942 +0.010254398771625728 20.756327386447293 +0.012297896890959432 21.444075865287108 +0.014748623620835866 22.14824329912942 +0.017687731539608613 22.868802295971808 +0.021212545323570628 23.60569555781095 +0.02543978452504797 24.358834661344513 +0.030509428586193463 25.128098915709195 +0.03658935207330667 25.913334309583036 +0.0438808836213417 26.71435256007565 +0.052625472665707156 27.530930275791356 +0.06311268472137505 28.362808246266862 +0.07568978996240554 29.20969086964743 +0.09077326261503152 30.071245729965067 +0.1088625719515157 30.947103334714765 +0.13055672155532347 31.83685702258569 +0.15657408453353153 32.74006305019484 +0.18777619149332744 33.656240865492414 +0.22519625899002232 34.584873574168654 +0.2700734031284433 35.52540860389958 +0.32389367125592594 36.47725856963797 +0.38843925045721495 37.4398023414018 +0.46584748232558293 38.41238631415587 +0.558681638206352 39.39432587744566 +0.6700157985415216 40.38490708045244 +0.8035366469828779 41.38338848612199 +0.9636655500511652 42.38900320600694 +1.155704964847984 43.400961105486616 +1.3860140229183928 44.41845116711778 +1.662219104491871 45.440643998059684 +1.9934663759895028 46.466694465836426 +2.390724653243303 47.495744445177905 +2.8671486193431552 48.52692565734757 +3.4385144245905592 49.559362582240816 +4.123742092876241 50.59217542264719 +4.9455220332787135 51.624483099425674 +5.931066402987885 52.655406255960436 +7.1130102019442685 53.68407025014819 +8.53049193775258 54.70960811232393 +10.230449645660688 55.7311634479528 +12.269175179593793 56.74789326459676 +14.714178242537946 57.758970703590784 +17.646421881176952 58.76358765801967 +21.16300347023456 59.760957259949166 +25.380369963776985 60.75031622141157 +30.4381738822752 61.730927015347156 +36.50389772134529 62.70207988453025 +43.77839991335358 63.663094668429835 +52.502565989078875 64.6133224399387 +62.96528518386472 65.55214694592013 +75.51301662303693 66.47898584753494 +90.56126185818155 67.39329175829673 +108.60832365216545 68.29455307972847 +130.2518066168911 69.18229463633746 +156.20840610061043 70.05607811336218 +187.33764060765768 70.91550230235657 +224.6703136183316 71.76020316114777 +269.4426472844996 72.58985369602001 +323.13721829315955 73.40416367513063 +387.5320514350058 74.20287918314912 +464.7594965466816 74.98578202792392 +557.3768384588742 75.75268901062408 +668.4509781054145 76.50345107127943 +801.6599888964605 77.23795232195741 +961.4149112608915 77.95610897997565 +1153.0058184233135 78.65786821356829 +1382.776990190932 79.34320691230987 +1658.3369953988358 80.01213039436676 +1988.8106396163741 80.66467106230726 +2385.141121030115 81.30088701876743 +2860.452399996279 81.92086065275878 +3430.483781651746 82.52469720682633 +4114.111102212703 83.11252333463494 +4933.971777356766 83.68448565789306 +5917.214410340096 84.24074933082515 +7096.397782131982 84.78149661968979 +8510.568992437999 85.30692550412014 +10206.556452827102 85.81724830634437 +12240.520547722415 86.31269035363641 +14679.813311345897 86.79348867865724 +17605.208701362422 87.25989076167984 +21113.577321788955 87.71215331805303 +25321.094165084287 88.15054113365383 +30367.085593562508 88.5753259505081 +36418.64294783653 88.98678540422648 +43676.155555841964 89.38520201441052 +52379.94636072586 89.77086222873115 +62818.22989765275 90.14405552096902 +75336.65613741691 90.50507354293457 +90349.75622863708 90.85420932985255 +108354.66914916379 91.19175655850067 +129947.60380663238 91.51800885713408 +155843.581708872 91.83325916600391 +186900.1139566247 92.13779914708759 +224145.59659090926 92.43191864148895 diff --git a/benchmark/RustQC/large/dupradar/GM12878_REP1.markdup.sorted_expressionHist.png b/benchmark/RustQC/large/dupradar/GM12878_REP1.markdup.sorted_expressionHist.png index e3029f6..dfe4572 100644 Binary files a/benchmark/RustQC/large/dupradar/GM12878_REP1.markdup.sorted_expressionHist.png and b/benchmark/RustQC/large/dupradar/GM12878_REP1.markdup.sorted_expressionHist.png differ diff --git a/benchmark/RustQC/large/dupradar/GM12878_REP1.markdup.sorted_expressionHist.svg b/benchmark/RustQC/large/dupradar/GM12878_REP1.markdup.sorted_expressionHist.svg index 8967d39..412f446 100644 --- a/benchmark/RustQC/large/dupradar/GM12878_REP1.markdup.sorted_expressionHist.svg +++ b/benchmark/RustQC/large/dupradar/GM12878_REP1.markdup.sorted_expressionHist.svg @@ -14,196 +14,198 @@ reads per kilobase (RPK) 0 - + 200 - - + + 400 - - + + 600 - - + + 800 - - + + 1000 - + - + 0.01 - - + + 0.1 - - + + 1 - - + + 10 - - + + 100 - - + + 1000 - - + + 1e+04 - - + + 1e+05 - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - + + + diff --git a/benchmark/RustQC/large/dupradar/GM12878_REP1.markdup.sorted_intercept_slope.txt b/benchmark/RustQC/large/dupradar/GM12878_REP1.markdup.sorted_intercept_slope.txt index 46e520a..dbc4021 100644 --- a/benchmark/RustQC/large/dupradar/GM12878_REP1.markdup.sorted_intercept_slope.txt +++ b/benchmark/RustQC/large/dupradar/GM12878_REP1.markdup.sorted_intercept_slope.txt @@ -1,2 +1,2 @@ -intercept 0.8245216334168248 -slope 1.677389460716357 +intercept 0.7419969763829039 +slope 1.6879062344542224 diff --git a/benchmark/RustQC/large/featurecounts/GM12878_REP1.markdup.sorted.featureCounts.tsv b/benchmark/RustQC/large/featurecounts/GM12878_REP1.markdup.sorted.featureCounts.tsv index c3edbde..0a07032 100644 --- a/benchmark/RustQC/large/featurecounts/GM12878_REP1.markdup.sorted.featureCounts.tsv +++ b/benchmark/RustQC/large/featurecounts/GM12878_REP1.markdup.sorted.featureCounts.tsv @@ -1,4 +1,4 @@ -# Program:RustQC v0.1.0; Command:"rustqc rna benchmark/input/large/GM12878_REP1.markdup.sorted.bam --gtf benchmark/input/large/genes.gtf.gz -s 0 -p -t 10 -o benchmark/RustQC/large/ -c benchmark/input/large/config.yaml" +# Program:RustQC v0.1.0; Command:"rustqc rna /Users/ewels/GitHub/seqera/RustQC/benchmark/input/large/GM12878_REP1.markdup.sorted.bam --gtf /Users/ewels/GitHub/seqera/RustQC/benchmark/input/large/genes.gtf.gz -s 0 -t 8 -o /tmp/rustqc_final_run -c /Users/ewels/GitHub/seqera/RustQC/benchmark/input/large/config.yaml --biotype-attribute gene_type" Geneid Chr Start End Strand Length GM12878_REP1.markdup.sorted.bam ENSG00000290825.1 chr1;chr1;chr1 11869;12613;13221 12227;12721;14409 +;+;+ 1657 0 ENSG00000223972.6 chr1;chr1;chr1;chr1;chr1;chr1 12010;12179;12613;12975;13221;13453 12057;12227;12697;13052;13374;13670 +;+;+;+;+;+ 632 0 diff --git a/benchmark/RustQC/large/preseq/GM12878_REP1.markdup.sorted.lc_extrap.txt b/benchmark/RustQC/large/preseq/GM12878_REP1.markdup.sorted.lc_extrap.txt index d989509..7c540b8 100644 --- a/benchmark/RustQC/large/preseq/GM12878_REP1.markdup.sorted.lc_extrap.txt +++ b/benchmark/RustQC/large/preseq/GM12878_REP1.markdup.sorted.lc_extrap.txt @@ -1,10002 +1,10002 @@ TOTAL_READS EXPECTED_DISTINCT LOWER_0.95CI UPPER_0.95CI 0.0 0.0 0.0 0.0 -1000000.0 897331.6 895859.5 899559.9 -2000000.0 1704183.8 1701496.5 1708487.0 -3000000.0 2450443.8 2446703.6 2456603.0 -4000000.0 3147306.0 3142586.3 3155091.8 -5000000.0 3801712.4 3796070.9 3810907.6 -6000000.0 4418638.4 4412166.4 4429086.3 -7000000.0 5001958.0 4994768.0 5013556.6 -8000000.0 5554901.7 5547070.4 5567534.1 -9000000.0 6080160.7 6071754.5 6093723.4 -10000000.0 6580039.5 6571119.7 6594442.5 -11000000.0 7056548.8 7047165.1 7071709.2 -12000000.0 7511461.1 7501668.9 7527306.4 -13000000.0 7946344.7 7936190.2 7962812.0 -14000000.0 8362601.3 8352131.5 8379638.5 -15000000.0 8761507.1 8750758.1 8779065.5 -16000000.0 9144207.5 9133210.9 9162234.9 -17000000.0 9511744.8 9500527.5 9530186.8 -18000000.0 9865058.0 9853654.0 9883865.1 -19000000.0 10205024.7 10193452.0 10224162.6 -20000000.0 10532434.7 10520717.0 10551867.5 -21000000.0 10848021.4 10836176.1 10867723.3 -22000000.0 11152461.6 11140503.4 11172401.6 -23000000.0 11446370.6 11434318.8 11466527.5 -24000000.0 11730340.1 11718193.9 11750680.3 -25000000.0 12004894.2 11992664.6 12025392.8 -26000000.0 12270523.5 12258223.8 12291162.1 -27000000.0 12527689.5 12515330.2 12548453.7 -28000000.0 12776823.6 12764410.9 12797697.1 -29000000.0 13018322.9 13005868.5 13039292.9 -30000000.0 13252562.9 13240073.4 13273616.4 -31000000.0 13479893.6 13467376.6 13501017.0 -32000000.0 13700640.7 13688102.5 13721825.3 -33000000.0 13915112.4 13902557.3 13936347.6 -34000000.0 14123594.9 14111029.6 14144872.9 -35000000.0 14326359.1 14313788.7 14347673.5 -36000000.0 14523660.5 14511087.4 14545001.7 -37000000.0 14715730.2 14703165.1 14737098.1 -38000000.0 14902797.9 14890247.1 14924188.6 -39000000.0 15085077.2 15072544.4 15106486.0 -40000000.0 15262768.3 15250257.2 15284190.6 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b/benchmark/RustQC/large/qualimap/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt @@ -0,0 +1,101 @@ +#Transcript position Transcript coverage profile +0.0 460513.37092936895 +1.0 491611.40275044704 +2.0 519571.7623978977 +3.0 536588.2698504555 +4.0 549037.3476701035 +5.0 564785.6661868759 +6.0 579476.2083242387 +7.0 591395.6839191682 +8.0 599203.7584960238 +9.0 611554.552057536 +10.0 620288.0912699214 +11.0 626524.4372566339 +12.0 630473.447150857 +13.0 632652.6706772218 +14.0 629600.7209527275 +15.0 632944.5119831604 +16.0 633590.4598740607 +17.0 636332.2887724125 +18.0 639294.6817091902 +19.0 640862.6240343485 +20.0 648728.1278858092 +21.0 656440.8774667544 +22.0 662391.4719821435 +23.0 664138.8348278198 +24.0 668791.2375184094 +25.0 677479.2805060586 +26.0 681314.7359191205 +27.0 679730.9625299763 +28.0 676068.513668197 +29.0 673867.7169491423 +30.0 671307.8983253543 +31.0 666809.673432354 +32.0 664730.830601566 +33.0 667516.1004504315 +34.0 668171.5299294392 +35.0 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+77.0 567969.5545966332 +78.0 562531.1996741627 +79.0 560227.5559798118 +80.0 556244.1816876075 +81.0 551805.4074955799 +82.0 545804.4690609905 +83.0 541847.0908759908 +84.0 532730.0262332875 +85.0 525195.812821797 +86.0 512509.3988975241 +87.0 499991.22702301526 +88.0 480851.3460907314 +89.0 459351.6451369649 +90.0 431647.2480801305 +91.0 397513.95497731335 +92.0 363104.4525543993 +93.0 320426.12083143706 +94.0 279742.9996204194 +95.0 235507.74505896133 +96.0 182075.09430133435 +97.0 129771.68532027332 +98.0 78571.27820598621 +99.0 24568.07092263944 diff --git a/benchmark/RustQC/large/qualimap/rnaseq_qc_results.txt b/benchmark/RustQC/large/qualimap/rnaseq_qc_results.txt index c7671bd..3e78dff 100644 --- a/benchmark/RustQC/large/qualimap/rnaseq_qc_results.txt +++ b/benchmark/RustQC/large/qualimap/rnaseq_qc_results.txt @@ -1,26 +1,57 @@ +RNA-Seq QC report +----------------------------------- + >>>>>>> Input - bam file = GM12878_REP1.markdup.sorted + bam file = /Users/ewels/GitHub/seqera/RustQC/benchmark/input/large/GM12878_REP1.markdup.sorted.bam + gff file = /Users/ewels/Library/CloudStorage/SeqeraDesktop-Fusion/Amazon S3/nf-core-awsmegatests/testing/rustqc/genes.filtered.gtf + counting algorithm = uniquely-mapped-reads + protocol = strand-specific-reverse + 5'-3' bias region size = 100 + 5'-3' bias number of top transcripts = 1000 + >>>>>>> Reads alignment - reads aligned = 175,097,721 - total alignments = 185,718,543 - secondary alignments = 10,620,822 - non-unique alignments = 10,620,822 - aligned to genes = 16,061,453 - ambiguous alignments = 1,277,361 - no feature assigned = 75,375,961 + reads aligned (left/right) = 87,559,392 / 87,538,329 + read pairs aligned = 87,420,177 + total alignments = 185,718,543 + secondary alignments = 10,620,822 + non-unique alignments = 17,723,193 + aligned to genes = 126,404,800 + ambiguous alignments = 2,552,785 + no feature assigned = 39,037,765 + not aligned = 0 + >>>>>>> Reads genomic origin - exonic = 744,941,713 (8.29%) - intronic = 837,462,849 (9.32%) - intergenic = 7,406,659,875 (82.40%) - overlapping exon = 1,700,860 (10.59%) + exonic = 126,404,800 (76.4%) + intronic = 30,407,985 (18.38%) + intergenic = 8,629,780 (5.22%) + overlapping exon = 6,853,516 (4.14%) + >>>>>>> Transcript coverage profile - 5' bias = 1.20 - 3' bias = 0.92 - 5'-3' bias = 1.24 + 5' bias = 0.87 + 3' bias = 0.78 + 5'-3' bias = 1.11 + + +>>>>>>> Junction analysis + + reads at junctions = 60,467,173 + + ACCT : 5.59% + AGGT : 5.41% + AGGA : 3.49% + TCCT : 3.19% + ATCT : 3.07% + AGGC : 2.88% + AGCT : 2.84% + GCCT : 2.58% + AGGG : 2.31% + CCCT : 2.27% + AGAT : 2.04% + diff --git a/benchmark/RustQC/large/rseqc/infer_experiment/GM12878_REP1.markdup.sorted.infer_experiment.txt b/benchmark/RustQC/large/rseqc/infer_experiment/GM12878_REP1.markdup.sorted.infer_experiment.txt index 00f82bb..ff09164 100644 --- a/benchmark/RustQC/large/rseqc/infer_experiment/GM12878_REP1.markdup.sorted.infer_experiment.txt +++ b/benchmark/RustQC/large/rseqc/infer_experiment/GM12878_REP1.markdup.sorted.infer_experiment.txt @@ -1,5 +1,5 @@ This is PairEnd Data -Fraction of reads failed to determine: 0.0819 -Fraction of reads explained by "1++,1--,2+-,2-+": 0.2196 -Fraction of reads explained by "1+-,1-+,2++,2--": 0.6986 +Fraction of reads failed to determine: 0.0792 +Fraction of reads explained by "1++,1--,2+-,2-+": 0.2364 +Fraction of reads explained by "1+-,1-+,2++,2--": 0.6844 diff --git a/benchmark/RustQC/large/rseqc/inner_distance/GM12878_REP1.markdup.sorted.inner_distance_freq.txt b/benchmark/RustQC/large/rseqc/inner_distance/GM12878_REP1.markdup.sorted.inner_distance_freq.txt index de62c5c..1caaf22 100644 --- a/benchmark/RustQC/large/rseqc/inner_distance/GM12878_REP1.markdup.sorted.inner_distance_freq.txt +++ b/benchmark/RustQC/large/rseqc/inner_distance/GM12878_REP1.markdup.sorted.inner_distance_freq.txt @@ -27,74 +27,74 @@ -120 -115 0 -115 -110 0 -110 -105 0 --105 -100 662 --100 -95 3513 --95 -90 3870 --90 -85 4323 --85 -80 4526 --80 -75 5278 --75 -70 6793 --70 -65 9054 --65 -60 11543 --60 -55 14363 --55 -50 17298 --50 -45 20762 --45 -40 24973 --40 -35 31008 --35 -30 42340 --30 -25 61344 --25 -20 92049 --20 -15 140275 --15 -10 205531 --10 -5 287459 --5 0 392945 -0 5 479038 -5 10 577055 -10 15 649757 -15 20 702144 -20 25 717534 -25 30 706688 -30 35 663711 -35 40 600349 -40 45 524206 -45 50 444275 -50 55 366309 -55 60 292165 -60 65 226098 -65 70 168571 -70 75 120923 -75 80 83700 -80 85 55161 -85 90 35651 -90 95 23989 -95 100 17577 -100 105 14130 -105 110 12995 -110 115 13013 -115 120 12245 -120 125 14011 -125 130 12357 -130 135 12526 -135 140 12095 -140 145 12284 -145 150 11790 -150 155 11508 -155 160 11145 -160 165 10089 -165 170 9420 -170 175 8222 -175 180 7833 -180 185 6936 -185 190 6300 -190 195 5998 -195 200 5856 -200 205 5275 -205 210 4995 -210 215 6927 -215 220 4701 -220 225 4980 -225 230 4632 -230 235 4382 -235 240 4592 -240 245 4498 -245 250 4929 +-105 -100 544 +-100 -95 2912 +-95 -90 3204 +-90 -85 3558 +-85 -80 3702 +-80 -75 4337 +-75 -70 5556 +-70 -65 7376 +-65 -60 9448 +-60 -55 11810 +-55 -50 14289 +-50 -45 17014 +-45 -40 20377 +-40 -35 25631 +-35 -30 34730 +-30 -25 50300 +-25 -20 75560 +-20 -15 115083 +-15 -10 168879 +-10 -5 235002 +-5 0 322485 +0 5 393930 +5 10 473111 +10 15 531131 +15 20 572151 +20 25 583050 +25 30 572553 +30 35 536412 +35 40 484471 +40 45 421747 +45 50 355491 +50 55 293277 +55 60 232429 +60 65 180172 +65 70 133950 +70 75 95969 +75 80 66627 +80 85 43182 +85 90 28471 +90 95 19106 +95 100 14161 +100 105 11898 +105 110 10542 +110 115 10492 +115 120 10185 +120 125 11212 +125 130 10700 +130 135 11068 +135 140 10597 +140 145 11205 +145 150 10743 +150 155 10964 +155 160 10371 +160 165 9114 +165 170 8447 +170 175 7595 +175 180 6751 +180 185 6170 +185 190 5932 +190 195 5305 +195 200 5068 +200 205 4193 +205 210 4070 +210 215 6178 +215 220 4066 +220 225 4154 +225 230 4141 +230 235 3947 +235 240 4018 +240 245 4006 +245 250 4540 diff --git a/benchmark/RustQC/large/rseqc/inner_distance/GM12878_REP1.markdup.sorted.inner_distance_plot.png b/benchmark/RustQC/large/rseqc/inner_distance/GM12878_REP1.markdup.sorted.inner_distance_plot.png index f66cd2b..d74dc6c 100644 Binary files a/benchmark/RustQC/large/rseqc/inner_distance/GM12878_REP1.markdup.sorted.inner_distance_plot.png and b/benchmark/RustQC/large/rseqc/inner_distance/GM12878_REP1.markdup.sorted.inner_distance_plot.png differ diff --git a/benchmark/RustQC/large/rseqc/inner_distance/GM12878_REP1.markdup.sorted.inner_distance_plot.r b/benchmark/RustQC/large/rseqc/inner_distance/GM12878_REP1.markdup.sorted.inner_distance_plot.r index 4000ea4..94eec82 100644 --- a/benchmark/RustQC/large/rseqc/inner_distance/GM12878_REP1.markdup.sorted.inner_distance_plot.r +++ b/benchmark/RustQC/large/rseqc/inner_distance/GM12878_REP1.markdup.sorted.inner_distance_plot.r @@ -1,6 +1,6 @@ -out_file = 'benchmark/RustQC/large/rseqc/inner_distance/GM12878_REP1.markdup.sorted' -pdf('benchmark/RustQC/large/rseqc/inner_distance/GM12878_REP1.markdup.sorted.inner_distance_plot.pdf') -fragsize=rep(c(-247.5,-242.5,-237.5,-232.5,-227.5,-222.5,-217.5,-212.5,-207.5,-202.5,-197.5,-192.5,-187.5,-182.5,-177.5,-172.5,-167.5,-162.5,-157.5,-152.5,-147.5,-142.5,-137.5,-132.5,-127.5,-122.5,-117.5,-112.5,-107.5,-102.5,-97.5,-92.5,-87.5,-82.5,-77.5,-72.5,-67.5,-62.5,-57.5,-52.5,-47.5,-42.5,-37.5,-32.5,-27.5,-22.5,-17.5,-12.5,-7.5,-2.5,2.5,7.5,12.5,17.5,22.5,27.5,32.5,37.5,42.5,47.5,52.5,57.5,62.5,67.5,72.5,77.5,82.5,87.5,92.5,97.5,102.5,107.5,112.5,117.5,122.5,127.5,132.5,137.5,142.5,147.5,152.5,157.5,162.5,167.5,172.5,177.5,182.5,187.5,192.5,197.5,202.5,207.5,212.5,217.5,222.5,227.5,232.5,237.5,242.5,247.5),times=c(0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,662,3513,3870,4323,4526,5278,6793,9054,11543,14363,17298,20762,24973,31008,42340,61344,92049,140275,205531,287459,392945,479038,577055,649757,702144,717534,706688,663711,600349,524206,444275,366309,292165,226098,168571,120923,83700,55161,35651,23989,17577,14130,12995,13013,12245,14011,12357,12526,12095,12284,11790,11508,11145,10089,9420,8222,7833,6936,6300,5998,5856,5275,4995,6927,4701,4980,4632,4382,4592,4498,4929)) +out_file = '/tmp/rustqc_final_run/rseqc/inner_distance/GM12878_REP1.markdup.sorted' +pdf('/tmp/rustqc_final_run/rseqc/inner_distance/GM12878_REP1.markdup.sorted.inner_distance_plot.pdf') +fragsize=rep(c(-247.5,-242.5,-237.5,-232.5,-227.5,-222.5,-217.5,-212.5,-207.5,-202.5,-197.5,-192.5,-187.5,-182.5,-177.5,-172.5,-167.5,-162.5,-157.5,-152.5,-147.5,-142.5,-137.5,-132.5,-127.5,-122.5,-117.5,-112.5,-107.5,-102.5,-97.5,-92.5,-87.5,-82.5,-77.5,-72.5,-67.5,-62.5,-57.5,-52.5,-47.5,-42.5,-37.5,-32.5,-27.5,-22.5,-17.5,-12.5,-7.5,-2.5,2.5,7.5,12.5,17.5,22.5,27.5,32.5,37.5,42.5,47.5,52.5,57.5,62.5,67.5,72.5,77.5,82.5,87.5,92.5,97.5,102.5,107.5,112.5,117.5,122.5,127.5,132.5,137.5,142.5,147.5,152.5,157.5,162.5,167.5,172.5,177.5,182.5,187.5,192.5,197.5,202.5,207.5,212.5,217.5,222.5,227.5,232.5,237.5,242.5,247.5),times=c(0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,544,2912,3204,3558,3702,4337,5556,7376,9448,11810,14289,17014,20377,25631,34730,50300,75560,115083,168879,235002,322485,393930,473111,531131,572151,583050,572553,536412,484471,421747,355491,293277,232429,180172,133950,95969,66627,43182,28471,19106,14161,11898,10542,10492,10185,11212,10700,11068,10597,11205,10743,10964,10371,9114,8447,7595,6751,6170,5932,5305,5068,4193,4070,6178,4066,4154,4141,3947,4018,4006,4540)) frag_sd = sd(fragsize) frag_mean = mean(fragsize) frag_median = median(fragsize) diff --git a/benchmark/RustQC/large/rseqc/inner_distance/GM12878_REP1.markdup.sorted.inner_distance_plot.svg b/benchmark/RustQC/large/rseqc/inner_distance/GM12878_REP1.markdup.sorted.inner_distance_plot.svg index 8c409a1..0b85776 100644 --- a/benchmark/RustQC/large/rseqc/inner_distance/GM12878_REP1.markdup.sorted.inner_distance_plot.svg +++ b/benchmark/RustQC/large/rseqc/inner_distance/GM12878_REP1.markdup.sorted.inner_distance_plot.svg @@ -1,7 +1,7 @@ -Mean= 28.2238 ; SD= 34.8091 +Mean= 28.2868 ; SD= 35.4439 @@ -163,7 +163,7 @@ Mean= 28.2238 ; SD= 34.8091 - + @@ -303,8 +303,8 @@ mRNA insert size (bp) - - + + @@ -325,58 +325,58 @@ mRNA insert size (bp) - - + + - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -397,18 +397,18 @@ mRNA insert size (bp) - - + + - - - - + + + + - - + + @@ -419,8 +419,8 @@ mRNA insert size (bp) - - + + @@ -441,5 +441,5 @@ mRNA insert size (bp) - + diff --git a/benchmark/RustQC/large/rseqc/inner_distance/GM12878_REP1.markdup.sorted.inner_distance_summary.txt b/benchmark/RustQC/large/rseqc/inner_distance/GM12878_REP1.markdup.sorted.inner_distance_summary.txt index c88ccd0..ef6ea97 100644 --- a/benchmark/RustQC/large/rseqc/inner_distance/GM12878_REP1.markdup.sorted.inner_distance_summary.txt +++ b/benchmark/RustQC/large/rseqc/inner_distance/GM12878_REP1.markdup.sorted.inner_distance_summary.txt @@ -1,9 +1,9 @@ -Total read pairs: 9840640 +Total read pairs: 8000000 Different chromosome: 0 -Different transcript: 2870259 -Same exon (mRNA distance): 928097 -Different exon (mRNA distance): 338053 -Non-exonic (genomic distance): 4720173 +Different transcript: 2313116 +Same exon (mRNA distance): 607516 +Different exon (mRNA distance): 260579 +Non-exonic (genomic distance): 4009786 Unknown chromosome: 0 -Read pair overlap: 984058 -Mean inner distance: 28.22 +Read pair overlap: 809003 +Mean inner distance: 28.29 diff --git a/benchmark/RustQC/large/rseqc/junction_annotation/GM12878_REP1.markdup.sorted.junction_plot.r b/benchmark/RustQC/large/rseqc/junction_annotation/GM12878_REP1.markdup.sorted.junction_plot.r index 861b075..ea00177 100644 --- a/benchmark/RustQC/large/rseqc/junction_annotation/GM12878_REP1.markdup.sorted.junction_plot.r +++ b/benchmark/RustQC/large/rseqc/junction_annotation/GM12878_REP1.markdup.sorted.junction_plot.r @@ -1,8 +1,8 @@ -pdf("benchmark/RustQC/large/rseqc/junction_annotation/GM12878_REP1.markdup.sorted.splice_events.pdf") +pdf("/tmp/rustqc_final_run/rseqc/junction_annotation/GM12878_REP1.markdup.sorted.splice_events.pdf") events=c(0.054,99.156,0.790) pie(events,col=c(2,3,4),init.angle=30,angle=c(60,120,150),density=c(70,70,70),main="splicing events",labels=c("partial_novel 0%","complete_novel 99%","known 1%")) dev.off() -pdf("benchmark/RustQC/large/rseqc/junction_annotation/GM12878_REP1.markdup.sorted.splice_junction.pdf") +pdf("/tmp/rustqc_final_run/rseqc/junction_annotation/GM12878_REP1.markdup.sorted.splice_junction.pdf") junction=c(0.237,99.200,0.563) pie(junction,col=c(2,3,4),init.angle=30,angle=c(60,120,150),density=c(70,70,70),main="splicing junctions",labels=c("partial_novel 0%","complete_novel 99%","known 1%")) dev.off() diff --git a/benchmark/RustQC/large/rseqc/junction_saturation/GM12878_REP1.markdup.sorted.junctionSaturation_plot.png b/benchmark/RustQC/large/rseqc/junction_saturation/GM12878_REP1.markdup.sorted.junctionSaturation_plot.png index 8fde17e..21c776d 100644 Binary files a/benchmark/RustQC/large/rseqc/junction_saturation/GM12878_REP1.markdup.sorted.junctionSaturation_plot.png and b/benchmark/RustQC/large/rseqc/junction_saturation/GM12878_REP1.markdup.sorted.junctionSaturation_plot.png differ diff --git a/benchmark/RustQC/large/rseqc/junction_saturation/GM12878_REP1.markdup.sorted.junctionSaturation_plot.r b/benchmark/RustQC/large/rseqc/junction_saturation/GM12878_REP1.markdup.sorted.junctionSaturation_plot.r index cf3c31e..3f8b5d7 100644 --- a/benchmark/RustQC/large/rseqc/junction_saturation/GM12878_REP1.markdup.sorted.junctionSaturation_plot.r +++ b/benchmark/RustQC/large/rseqc/junction_saturation/GM12878_REP1.markdup.sorted.junctionSaturation_plot.r @@ -1,8 +1,8 @@ -pdf('benchmark/RustQC/large/rseqc/junction_saturation/GM12878_REP1.markdup.sorted.junctionSaturation_plot.pdf') +pdf('/tmp/rustqc_final_run/rseqc/junction_saturation/GM12878_REP1.markdup.sorted.junctionSaturation_plot.pdf') x=c(5,10,15,20,25,30,35,40,45,50,55,60,65,70,75,80,85,90,95,100) -y=c(834,953,1022,1079,1115,1136,1166,1185,1207,1223,1235,1250,1261,1277,1292,1303,1311,1320,1328,1330) -z=c(109136,134083,149872,161877,172009,180824,188666,195901,202697,208963,214833,220300,225643,230477,235269,239859,244202,248561,252574,256392) -w=c(108302,133130,148850,160798,170894,179688,187500,194716,201490,207740,213598,219050,224382,229200,233977,238556,242891,247241,251246,255062) +y=c(842,965,1036,1080,1112,1142,1163,1186,1202,1223,1239,1258,1270,1276,1287,1290,1297,1306,1320,1330) +z=c(109083,133824,149472,161566,171925,180826,188844,196018,202788,208991,214823,220336,225627,230514,235209,239768,244119,248455,252571,256392) +w=c(108241,132859,148436,160486,170813,179684,187681,194832,201586,207768,213584,219078,224357,229238,233922,238478,242822,247149,251251,255062) m=max(256,256,255) n=min(0,109,108) plot(x,z/1000,xlab='percent of total reads',ylab='Number of splicing junctions (x1000)',type='o',col='blue',ylim=c(n,m)) diff --git a/benchmark/RustQC/large/rseqc/junction_saturation/GM12878_REP1.markdup.sorted.junctionSaturation_plot.svg b/benchmark/RustQC/large/rseqc/junction_saturation/GM12878_REP1.markdup.sorted.junctionSaturation_plot.svg index fcbfe71..97d6600 100644 --- a/benchmark/RustQC/large/rseqc/junction_saturation/GM12878_REP1.markdup.sorted.junctionSaturation_plot.svg +++ b/benchmark/RustQC/large/rseqc/junction_saturation/GM12878_REP1.markdup.sorted.junctionSaturation_plot.svg @@ -238,10 +238,10 @@ Percent of total reads 100.0 - + - - + + @@ -250,16 +250,16 @@ Percent of total reads - + - + - + @@ -272,7 +272,7 @@ Percent of total reads - + @@ -280,21 +280,21 @@ Percent of total reads - + - - + + - + - + - + diff --git a/benchmark/RustQC/large/rseqc/junction_saturation/GM12878_REP1.markdup.sorted.junctionSaturation_summary.txt b/benchmark/RustQC/large/rseqc/junction_saturation/GM12878_REP1.markdup.sorted.junctionSaturation_summary.txt index 35f0c39..e5e42ce 100644 --- a/benchmark/RustQC/large/rseqc/junction_saturation/GM12878_REP1.markdup.sorted.junctionSaturation_summary.txt +++ b/benchmark/RustQC/large/rseqc/junction_saturation/GM12878_REP1.markdup.sorted.junctionSaturation_summary.txt @@ -1,21 +1,21 @@ Percent All_Junctions Known_Junctions Novel_Junctions -5 109136 834 108302 -10 134083 953 133130 -15 149872 1022 148850 -20 161877 1079 160798 -25 172009 1115 170894 -30 180824 1136 179688 -35 188666 1166 187500 -40 195901 1185 194716 -45 202697 1207 201490 -50 208963 1223 207740 -55 214833 1235 213598 -60 220300 1250 219050 -65 225643 1261 224382 -70 230477 1277 229200 -75 235269 1292 233977 -80 239859 1303 238556 -85 244202 1311 242891 -90 248561 1320 247241 -95 252574 1328 251246 +5 109083 842 108241 +10 133824 965 132859 +15 149472 1036 148436 +20 161566 1080 160486 +25 171925 1112 170813 +30 180826 1142 179684 +35 188844 1163 187681 +40 196018 1186 194832 +45 202788 1202 201586 +50 208991 1223 207768 +55 214823 1239 213584 +60 220336 1258 219078 +65 225627 1270 224357 +70 230514 1276 229238 +75 235209 1287 233922 +80 239768 1290 238478 +85 244119 1297 242822 +90 248455 1306 247149 +95 252571 1320 251251 100 256392 1330 255062 diff --git a/benchmark/RustQC/large/rseqc/tin/GM12878_REP1.markdup.sorted.summary.txt b/benchmark/RustQC/large/rseqc/tin/GM12878_REP1.markdup.sorted.summary.txt index 1ca3749..58a2f72 100644 --- a/benchmark/RustQC/large/rseqc/tin/GM12878_REP1.markdup.sorted.summary.txt +++ b/benchmark/RustQC/large/rseqc/tin/GM12878_REP1.markdup.sorted.summary.txt @@ -1,2 +1,2 @@ Bam_file TIN(mean) TIN(median) TIN(stdev) -benchmark/input/large/GM12878_REP1.markdup.sorted.bam 72.55 83.89 26.14 +/Users/ewels/GitHub/seqera/RustQC/benchmark/input/large/GM12878_REP1.markdup.sorted.bam 72.55 83.89 26.14 diff --git a/benchmark/RustQC/small/dupradar/test_dupMatrix.txt b/benchmark/RustQC/small/dupradar/test_dupMatrix.txt index d70ecf9..57ca4bb 100644 --- a/benchmark/RustQC/small/dupradar/test_dupMatrix.txt +++ b/benchmark/RustQC/small/dupradar/test_dupMatrix.txt @@ -2,13 +2,13 @@ ID geneLength allCountsMulti filteredCountsMulti dupRateMulti dupsPerIdMulti RPK ENSG00000271530 331 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000220212 938 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000170590 727 0 0 NA 0 0 0 0 0 NA 0 0 0 -ENSG00000217929 2812 1 1 0 0 0.355618776671408 13.4530822679658 0 0 NA 0 0 0 +ENSG00000217929 2812 1 1 0 0 0.355618776671408 6.73023290886293 0 0 NA 0 0 0 ENSG00000218577 709 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000263667 2050 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000205653 2007 0 0 NA 0 0 0 0 0 NA 0 0 0 -ENSG00000112679 5686 28 27 0.035714285714286 1 4.9243756595146 186.289462794681 28 27 0.035714285714286 1 4.9243756595146 186.289462794681 -ENSG00000137265 5898 276 262 0.050724637681159 14 46.795523906409 1770.27782047397 276 262 0.050724637681159 14 46.795523906409 1770.27782047397 -ENSG00000112685 4989 16 16 0 0 3.20705552214873 121.323126358051 16 16 0 0 3.20705552214873 121.323126358051 +ENSG00000112679 5686 56 54 0.035714285714286 2 9.84875131902919 186.391705350767 56 54 0.035714285714286 2 9.84875131902919 186.391705350767 +ENSG00000137265 5898 549 522 0.049180327868852 27 93.0824008138352 1761.6230589874 549 522 0.049180327868852 27 93.0824008138352 1761.6230589874 +ENSG00000112685 4989 32 32 0 0 6.41411104429745 121.389712982786 32 32 0 0 6.41411104429745 121.389712982786 ENSG00000230433 851 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000188996 1025 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000219712 1227 0 0 NA 0 0 0 0 0 NA 0 0 0 @@ -28,41 +28,41 @@ ENSG00000243439 295 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000218027 1592 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000272279 548 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000054598 3447 0 0 NA 0 0 0 0 0 NA 0 0 0 -ENSG00000112699 4304 11 9 0.181818181818182 2 2.55576208178439 96.6846516525833 11 9 0.181818181818182 2 2.55576208178439 96.6846516525833 -ENSG00000250903 13177 1 1 0 0 0.075889807998786 2.87091654682552 1 1 0 0 0.075889807998786 2.87091654682552 +ENSG00000112699 4304 22 18 0.181818181818182 4 5.11152416356877 96.7377157699573 22 18 0.181818181818182 4 5.11152416356877 96.7377157699573 +ENSG00000250903 13177 2 2 0 0 0.151779615997572 2.87249221214579 2 2 0 0 0.151779615997572 2.87249221214579 ENSG00000236086 267 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000266252 100 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000272465 701 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000164385 2434 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000228718 834 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000145949 5877 0 0 NA 0 0 0 0 0 NA 0 0 0 -ENSG00000124535 3877 8 8 0 0 2.06345112200155 78.0604948929995 8 8 0 0 2.06345112200155 78.0604948929995 +ENSG00000124535 3877 16 16 0 0 4.1269022440031 78.1033373834307 16 16 0 0 4.1269022440031 78.1033373834307 ENSG00000021355 3226 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000266750 77 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000230438 1455 0 0 NA 0 0 0 0 0 NA 0 0 0 -ENSG00000170542 4118 13 12 0.076923076923077 1 3.15687226809131 119.424690477843 13 12 0.076923076923077 1 3.15687226809131 119.424690477843 +ENSG00000170542 4118 26 24 0.076923076923077 2 6.31374453618261 119.490235170662 26 24 0.076923076923077 2 6.31374453618261 119.490235170662 ENSG00000232999 193 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000228365 484 0 0 NA 0 0 0 0 0 NA 0 0 0 -ENSG00000124570 3994 1 1 0 0 0.250375563345018 9.47172442101148 1 1 0 0 0.250375563345018 9.47172442101148 +ENSG00000124570 3994 2 2 0 0 0.500751126690035 9.47692285414249 2 2 0 0 0.500751126690035 9.47692285414249 ENSG00000244041 2811 0 0 NA 0 0 0 0 0 NA 0 0 0 -ENSG00000124588 2451 1 1 0 0 0.407996736026112 15.4345439973561 1 1 0 0 0.407996736026112 15.4345439973561 +ENSG00000124588 2451 2 2 0 0 0.815993472052224 15.4430150466932 2 2 0 0 0.815993472052224 15.4430150466932 ENSG00000224846 535 0 0 NA 0 0 0 0 0 NA 0 0 0 -ENSG00000270346 2597 3 3 0 0 1.15517905275318 43.7005013525451 3 3 0 0 1.15517905275318 43.7005013525451 +ENSG00000270346 2597 6 6 0 0 2.31035810550635 43.724485806059 6 6 0 0 2.31035810550635 43.724485806059 ENSG00000271361 631 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000261015 2635 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000232654 417 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000217707 377 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000229282 398 0 0 NA 0 0 0 0 0 NA 0 0 0 -ENSG00000137275 4231 9 9 0 0 2.12715670054361 80.4704812190212 9 9 0 0 2.12715670054361 80.4704812190212 +ENSG00000137275 4231 18 18 0 0 4.25431340108721 80.5146463991978 18 18 0 0 4.25431340108721 80.5146463991978 ENSG00000272277 850 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000222248 124 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000137274 5780 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000228170 695 0 0 NA 0 0 0 0 0 NA 0 0 0 -ENSG00000137267 1727 3 3 0 0 1.73711638679792 65.7152298856743 1 1 0 0 0.579038795599305 21.9050766285581 +ENSG00000137267 1727 6 6 0 0 3.47423277359583 65.7512968374843 2 2 0 0 1.15807759119861 21.9170989458281 ENSG00000216819 871 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000230269 1505 0 0 NA 0 0 0 0 0 NA 0 0 0 -ENSG00000137285 2194 2 2 0 0 0.911577028258888 34.48502036237 0 0 NA 0 0 0 -ENSG00000180822 10418 2 2 0 0 0.191975427145325 7.2624433360568 2 2 0 0 0.191975427145325 7.2624433360568 +ENSG00000137285 2194 4 4 0 0 1.82315405651778 34.5039470186373 0 0 NA 0 0 0 +ENSG00000180822 10418 4 4 0 0 0.383950854290651 7.26642923391152 4 4 0 0 0.383950854290651 7.26642923391152 ENSG00000137266 8898 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000272320 1989 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000228793 789 0 0 NA 0 0 0 0 0 NA 0 0 0 @@ -71,7 +71,7 @@ ENSG00000168994 2474 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000270504 2761 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000219992 436 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000238158 629 0 0 NA 0 0 0 0 0 NA 0 0 0 -ENSG00000145945 1932 1 1 0 0 0.5175983436853 19.5807801954037 1 1 0 0 0.5175983436853 19.5807801954037 +ENSG00000145945 1932 2 2 0 0 1.0351966873706 19.5915268527149 2 2 0 0 1.0351966873706 19.5915268527149 ENSG00000233068 640 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000260604 7070 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000218472 371 0 0 NA 0 0 0 0 0 NA 0 0 0 @@ -81,11 +81,11 @@ ENSG00000216657 1038 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000145965 1464 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000272248 490 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000230648 209 0 0 NA 0 0 0 0 0 NA 0 0 0 -ENSG00000112739 8016 44 42 0.045454545454545 2 5.48902195608782 207.650070215927 34 33 0.029411764705882 1 4.24151696606786 160.45687243958 +ENSG00000112739 8016 88 84 0.045454545454545 4 10.9780439121756 207.764036264419 68 66 0.029411764705882 2 8.48303393213573 160.544937113415 ENSG00000145975 3138 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000252668 85 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000185689 3322 0 0 NA 0 0 0 0 0 NA 0 0 0 -ENSG00000198721 4579 8 8 0 0 1.74710635509937 66.0931510592179 8 8 0 0 1.74710635509937 66.0931510592179 +ENSG00000198721 4579 5 5 0 0 1.0919414719371 20.6654454463011 5 5 0 0 1.0919414719371 20.6654454463011 ENSG00000254821 640 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000234817 2277 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000237716 266 0 0 NA 0 0 0 0 0 NA 0 0 0 @@ -98,7 +98,7 @@ ENSG00000260673 573 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000205444 484 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000238801 93 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000217385 1317 0 0 NA 0 0 0 0 0 NA 0 0 0 -ENSG00000153046 4531 7 7 0 0 1.54491282277643 58.4441561162302 7 7 0 0 1.54491282277643 58.4441561162302 +ENSG00000153046 4531 13 13 0 0 2.86912381372765 54.2993586882351 13 13 0 0 2.86912381372765 54.2993586882351 ENSG00000236336 369 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000217030 423 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000124787 1962 0 0 NA 0 0 0 0 0 NA 0 0 0 @@ -107,10 +107,10 @@ ENSG00000271978 3273 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000252419 518 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000220685 1188 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000219607 1736 0 0 NA 0 0 0 0 0 NA 0 0 0 -ENSG00000214113 9443 5 4 0.2 1 0.52949274594938 20.0307462339934 5 4 0.2 1 0.52949274594938 20.0307462339934 +ENSG00000214113 9443 10 8 0.2 2 1.05898549189876 20.0417398493302 10 8 0.2 2 1.05898549189876 20.0417398493302 ENSG00000265083 90 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000264541 70 0 0 NA 0 0 0 0 0 NA 0 0 0 -ENSG00000145982 2351 3 3 0 0 1.2760527435134 48.2731612133388 3 3 0 0 1.2760527435134 48.2731612133388 +ENSG00000145982 2351 6 6 0 0 2.5521054870268 48.2996553119248 6 6 0 0 2.5521054870268 48.2996553119248 ENSG00000220446 359 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000269985 1333 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000218574 969 0 0 NA 0 0 0 0 0 NA 0 0 0 @@ -122,52 +122,52 @@ ENSG00000239472 285 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000215057 1601 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000124785 1762 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000264121 102 0 0 NA 0 0 0 0 0 NA 0 0 0 -ENSG00000124491 4690 10 10 0 0 2.13219616204691 80.661124387036 10 10 0 0 2.13219616204691 80.661124387036 +ENSG00000124491 4690 20 20 0 0 4.26439232409382 80.7053941992433 20 20 0 0 4.26439232409382 80.7053941992433 ENSG00000263572 76 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000216863 5603 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000241216 301 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000218868 935 0 0 NA 0 0 0 0 0 NA 0 0 0 -ENSG00000112799 1254 37 35 0.054054054054054 2 29.5055821371611 1116.19815908153 37 35 0.054054054054054 2 29.5055821371611 1116.19815908153 +ENSG00000112799 1254 73 69 0.054794520547945 4 58.2137161084529 1101.71873253568 73 69 0.054794520547945 4 58.2137161084529 1101.71873253568 ENSG00000261211 3325 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000226281 568 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000224532 506 0 0 NA 0 0 0 0 0 NA 0 0 0 -ENSG00000219986 488 1 1 0 0 2.04918032786885 77.5206297899997 1 1 0 0 2.04918032786885 77.5206297899997 +ENSG00000219986 488 1 1 0 0 2.04918032786885 38.7815879912347 1 1 0 0 2.04918032786885 38.7815879912347 ENSG00000223342 933 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000240936 296 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000203498 517 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000251762 87 0 0 NA 0 0 0 0 0 NA 0 0 0 -ENSG00000124782 17254 11 11 0 0 0.637533325605657 24.117928637575 11 11 0 0 0.637533325605657 24.117928637575 +ENSG00000124782 17254 22 22 0 0 1.27506665121131 24.1311654499766 22 22 0 0 1.27506665121131 24.1311654499766 ENSG00000225092 1676 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000201483 105 0 0 NA 0 0 0 0 0 NA 0 0 0 -ENSG00000124783 11356 154 148 0.038961038961039 6 13.5611130679817 513.017820533468 152 146 0.039473684210526 6 13.3849947164495 506.35525143563 +ENSG00000124783 11356 289 279 0.034602076124567 10 25.4491017964072 481.634811340245 285 275 0.035087719298246 10 25.0968650933427 474.96858557775 ENSG00000238221 500 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000164304 3512 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000219375 391 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000220472 730 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000230570 1203 0 0 NA 0 0 0 0 0 NA 0 0 0 -ENSG00000124784 3237 10 10 0 0 3.08928019771393 116.867677903985 10 10 0 0 3.08928019771393 116.867677903985 +ENSG00000124784 3237 20 20 0 0 6.17856039542787 116.931819213609 20 20 0 0 6.17856039542787 116.931819213609 ENSG00000233503 1501 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000219993 347 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000234115 1241 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000261189 888 0 0 NA 0 0 0 0 0 NA 0 0 0 -ENSG00000096696 10093 1 1 0 0 0.099078569305459 3.74814894853065 1 1 0 0 0.099078569305459 3.74814894853065 -ENSG00000168566 5836 10 10 0 0 1.71350239890336 64.8219111335159 10 10 0 0 1.71350239890336 64.8219111335159 +ENSG00000096696 10093 2 2 0 0 0.198157138610918 3.75020607147975 2 2 0 0 0.198157138610918 3.75020607147975 +ENSG00000168566 5836 20 20 0 0 3.42700479780672 64.8574877989121 20 20 0 0 3.42700479780672 64.8574877989121 ENSG00000236512 457 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000153162 2780 0 0 NA 0 0 0 0 0 NA 0 0 0 -ENSG00000239264 4701 5 5 0 0 1.06360348861944 40.2361915948946 5 5 0 0 1.06360348861944 40.2361915948946 +ENSG00000239264 4701 9 9 0 0 1.914486279515 36.232447236227 9 9 0 0 1.914486279515 36.232447236227 ENSG00000259040 3030 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000217746 893 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000219294 1696 0 0 NA 0 0 0 0 0 NA 0 0 0 -ENSG00000188428 3315 6 6 0 0 1.80995475113122 68.4707101131581 6 6 0 0 1.80995475113122 68.4707101131581 +ENSG00000188428 3315 12 12 0 0 3.61990950226244 68.5082893745613 12 12 0 0 3.61990950226244 68.5082893745613 ENSG00000265818 768 0 0 NA 0 0 0 0 0 NA 0 0 0 -ENSG00000124802 2107 2 2 0 0 0.94921689606075 35.9089390958898 2 2 0 0 0.94921689606075 35.9089390958898 +ENSG00000124802 2107 2 2 0 0 0.94921689606075 17.9643236257452 2 2 0 0 0.94921689606075 17.9643236257452 ENSG00000232234 400 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000234763 746 0 0 NA 0 0 0 0 0 NA 0 0 0 -ENSG00000124786 2887 10 10 0 0 3.46380325597506 131.035910417457 10 10 0 0 3.46380325597506 131.035910417457 +ENSG00000124786 2887 20 20 0 0 6.92760651195012 131.10782777778 20 20 0 0 6.92760651195012 131.10782777778 ENSG00000251164 556 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000230939 489 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000225775 661 0 0 NA 0 0 0 0 0 NA 0 0 0 -ENSG00000181355 4783 1 1 0 0 0.209073803052478 7.90927604798659 1 1 0 0 0.209073803052478 7.90927604798659 +ENSG00000181355 4783 1 1 0 0 0.209073803052478 3.95680847579397 1 1 0 0 0.209073803052478 3.95680847579397 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0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000221021 94 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000227913 1350 0 0 NA 0 0 0 0 0 NA 0 0 0 @@ -2786,7 +2786,7 @@ ENSG00000225683 1131 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000239136 96 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000217514 254 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000270419 896 0 0 NA 0 0 0 0 0 NA 0 0 0 -ENSG00000112531 17368 22 22 0 0 1.26669737448181 47.9192469729063 22 22 0 0 1.26669737448181 47.9192469729063 +ENSG00000112531 17368 44 44 0 0 2.53339474896361 47.9455468302506 44 44 0 0 2.53339474896361 47.9455468302506 ENSG00000228692 602 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000235538 719 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000266128 290 0 0 NA 0 0 0 0 0 NA 0 0 0 @@ -2806,28 +2806,28 @@ ENSG00000223414 4376 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000252196 71 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000216624 1010 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000231297 1035 0 0 NA 0 0 0 0 0 NA 0 0 0 -ENSG00000164458 2629 2 2 0 0 0.760745530620008 28.7790546500722 2 2 0 0 0.760745530620008 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173.741514200732 ENSG00000261420 1636 0 0 NA 0 0 0 0 0 NA 0 0 0 -ENSG00000071242 8243 1 1 0 0 0.12131505519835 4.58935670720852 1 1 0 0 0.12131505519835 4.58935670720852 +ENSG00000071242 8243 2 2 0 0 0.2426301103967 4.59187551612824 2 2 0 0 0.2426301103967 4.59187551612824 ENSG00000232082 579 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000222958 80 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000269048 2341 0 0 NA 0 0 0 0 0 NA 0 0 0 -ENSG00000235272 354 2 1 0.5 1 5.64971751412429 213.729193997287 0 0 NA 0 0 0 +ENSG00000235272 354 3 2 0.333333333333333 1 8.47457627118644 160.38487237053 0 0 NA 0 0 0 ENSG00000235008 1746 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000249141 600 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000231654 627 0 0 NA 0 0 0 0 0 NA 0 0 0 -ENSG00000026297 7478 34 32 0.058823529411765 2 4.54667023268254 172.000841063877 34 32 0.058823529411765 2 4.54667023268254 172.000841063877 -ENSG00000197146 2298 6 6 0 0 2.61096605744125 98.7730217689814 6 6 0 0 2.61096605744125 98.7730217689814 +ENSG00000026297 7478 54 52 0.037037037037037 2 7.2211821342605 136.663868246191 54 52 0.037037037037037 2 7.2211821342605 136.663868246191 +ENSG00000197146 2298 11 11 0 0 4.78677110530896 90.5916293894465 11 11 0 0 4.78677110530896 90.5916293894465 ENSG00000227598 385 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000265828 106 0 0 NA 0 0 0 0 0 NA 0 0 0 -ENSG00000213066 15159 5 5 0 0 0.329837060492117 12.4777582088264 5 5 0 0 0.329837060492117 12.4777582088264 +ENSG00000213066 15159 8 8 0 0 0.527739296787387 9.98768517169869 8 8 0 0 0.527739296787387 9.98768517169869 ENSG00000272980 5310 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000112486 4226 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000166984 4332 0 0 NA 0 0 0 0 0 NA 0 0 0 @@ -2845,7 +2845,7 @@ ENSG00000213065 1486 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000146521 2146 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000269155 2718 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000198221 2362 0 0 NA 0 0 0 0 0 NA 0 0 0 -ENSG00000130396 13424 17 16 0.058823529411765 1 1.26638855780691 47.9075644173002 17 16 0.058823529411765 1 1.26638855780691 47.9075644173002 +ENSG00000130396 13424 34 32 0.058823529411765 2 2.53277711561383 47.9338578628253 34 32 0.058823529411765 2 2.53277711561383 47.9338578628253 ENSG00000235994 1539 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000229921 3088 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000125337 2797 0 0 NA 0 0 0 0 0 NA 0 0 0 @@ -2872,14 +2872,14 @@ ENSG00000233085 746 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000224999 866 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000226194 2685 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000272848 650 0 0 NA 0 0 0 0 0 NA 0 0 0 -ENSG00000184465 10259 4 4 0 0 0.389901549858661 14.7500018861565 4 4 0 0 0.389901549858661 14.7500018861565 +ENSG00000184465 10259 8 8 0 0 0.779803099717321 14.7580972334322 8 8 0 0 0.779803099717321 14.7580972334322 ENSG00000265654 86 0 0 NA 0 0 0 0 0 NA 0 0 0 -ENSG00000185127 4169 12 12 0 0 2.87838810266251 108.889615747239 12 12 0 0 2.87838810266251 108.889615747239 -ENSG00000130024 5388 12 12 0 0 2.2271714922049 84.254047522316 12 12 0 0 2.2271714922049 84.254047522316 +ENSG00000185127 4169 20 20 0 0 4.79731350443751 90.7911486674145 20 20 0 0 4.79731350443751 90.7911486674145 +ENSG00000130024 5388 24 24 0 0 4.4543429844098 84.3002892637976 24 24 0 0 4.4543429844098 84.3002892637976 ENSG00000232640 403 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000227704 335 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000184786 769 0 0 NA 0 0 0 0 0 NA 0 0 0 -ENSG00000130023 4251 10 9 0.1 1 2.35238767348859 88.9909840920251 10 9 0.1 1 2.35238767348859 88.9909840920251 +ENSG00000130023 4251 20 18 0.1 2 4.70477534697718 89.0398256397203 20 18 0.1 2 4.70477534697718 89.0398256397203 ENSG00000266896 1630 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000229214 2418 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000231690 2318 0 0 NA 0 0 0 0 0 NA 0 0 0 @@ -2890,14 +2890,14 @@ ENSG00000218716 490 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000230960 1330 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000271820 1953 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000227508 3611 0 0 NA 0 0 0 0 0 NA 0 0 0 -ENSG00000198719 3174 1 0 1 1 0.315059861373661 11.9187357711153 1 0 1 1 0.315059861373661 11.9187357711153 -ENSG00000112584 6029 15 15 0 0 2.48797478852214 94.1202537838444 13 13 0 0 2.15624481671919 81.5708866126652 +ENSG00000198719 3174 2 0 1 2 0.630119722747322 11.925277214696 2 0 1 2 0.630119722747322 11.925277214696 +ENSG00000112584 6029 28 28 0 0 4.64421960524133 87.8937831003867 24 24 0 0 3.98075966163543 75.33752837176 ENSG00000271234 500 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000266245 84 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000261003 5187 0 0 NA 0 0 0 0 0 NA 0 0 0 -ENSG00000008018 2256 68 66 0.029411764705882 2 30.1418439716312 1140.26798712383 66 64 0.03030303030303 2 29.2553191489362 1106.73069338489 -ENSG00000112592 2038 8 8 0 0 3.92541707556428 148.498792296447 8 8 0 0 3.92541707556428 148.498792296447 -ENSG00000071994 6476 9 9 0 0 1.38974675725757 52.5742134091536 9 9 0 0 1.38974675725757 52.5742134091536 +ENSG00000008018 2256 136 132 0.029411764705882 4 60.2836879432624 1140.89380842299 132 128 0.03030303030303 4 58.5106382978723 1107.33810817526 +ENSG00000112592 2038 15 15 0 0 7.36015701668302 139.294025562237 15 15 0 0 7.36015701668302 139.294025562237 +ENSG00000071994 6476 18 18 0 0 2.77949351451513 52.6030680844666 18 18 0 0 2.77949351451513 52.6030680844666 ENSG00000217874 931 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000234986 806 0 0 NA 0 0 0 0 0 NA 0 0 0 ENSG00000213863 758 0 0 NA 0 0 0 0 0 NA 0 0 0 diff --git a/benchmark/RustQC/small/dupradar/test_dup_intercept_mqc.txt b/benchmark/RustQC/small/dupradar/test_dup_intercept_mqc.txt index e5e67bc..dfa588c 100644 --- a/benchmark/RustQC/small/dupradar/test_dup_intercept_mqc.txt +++ b/benchmark/RustQC/small/dupradar/test_dup_intercept_mqc.txt @@ -9,4 +9,4 @@ # min: 0 # format: '{:.2f}' Sample dupRadar_intercept -test 0.031858934078430205 +test 0.027975359216305267 diff --git a/benchmark/RustQC/small/dupradar/test_duprateExpBoxplot.png b/benchmark/RustQC/small/dupradar/test_duprateExpBoxplot.png index 0e61886..99d0dde 100644 Binary files a/benchmark/RustQC/small/dupradar/test_duprateExpBoxplot.png and b/benchmark/RustQC/small/dupradar/test_duprateExpBoxplot.png differ diff --git a/benchmark/RustQC/small/dupradar/test_duprateExpBoxplot.svg b/benchmark/RustQC/small/dupradar/test_duprateExpBoxplot.svg index ebc6320..8d90f4a 100644 --- a/benchmark/RustQC/small/dupradar/test_duprateExpBoxplot.svg +++ b/benchmark/RustQC/small/dupradar/test_duprateExpBoxplot.svg @@ -128,16 +128,16 @@ mean expression (reads/kbp) 75 - 80 % / 0.0 -80 - 85 % / 0.7 +80 - 85 % / 1.2 -85 - 90 % / 1.6 +85 - 90 % / 3.2 -90 - 95 % / 3.5 +90 - 95 % / 6.8 -95 - 100 % / 40.4 +95 - 100 % / 79.0 @@ -147,7 +147,7 @@ mean expression (reads/kbp) - + @@ -161,7 +161,7 @@ mean expression (reads/kbp) - + @@ -175,14 +175,14 @@ mean expression (reads/kbp) - + - + - + @@ -205,27 +205,31 @@ mean expression (reads/kbp) - - + - + + - - + + - - + + + + + + - + - - + + - + @@ -234,12 +238,11 @@ mean expression (reads/kbp) - - - + + + - - + diff --git a/benchmark/RustQC/small/dupradar/test_duprateExpDens.png b/benchmark/RustQC/small/dupradar/test_duprateExpDens.png index 5d5adbb..489a080 100644 Binary files a/benchmark/RustQC/small/dupradar/test_duprateExpDens.png and b/benchmark/RustQC/small/dupradar/test_duprateExpDens.png differ diff --git a/benchmark/RustQC/small/dupradar/test_duprateExpDens.svg b/benchmark/RustQC/small/dupradar/test_duprateExpDens.svg index 16d5404..be49419 100644 --- a/benchmark/RustQC/small/dupradar/test_duprateExpDens.svg +++ b/benchmark/RustQC/small/dupradar/test_duprateExpDens.svg @@ -95,655 +95,670 @@ expression (reads/kbp) - -0.01 - - - - - - - + 0.1 - - + + - - + + 1 - - + + - - + + 10 - - + + - - + + 100 - - + + - - + + 1000 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + +1e+04 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Int: 0.03 -Sl: 1.60 +Sl: 1.58 diff --git a/benchmark/RustQC/small/dupradar/test_duprateExpDensCurve_mqc.txt b/benchmark/RustQC/small/dupradar/test_duprateExpDensCurve_mqc.txt index c874337..cc5a1cc 100644 --- a/benchmark/RustQC/small/dupradar/test_duprateExpDensCurve_mqc.txt +++ b/benchmark/RustQC/small/dupradar/test_duprateExpDensCurve_mqc.txt @@ -10,104 +10,104 @@ # ymax: 100 # xlog: True RPK Duplication Rate (%) -0.07588980799878577 1.8449904249827471 -0.0833728519762587 1.8801645061104135 -0.09159375454957483 1.9159960786705732 -0.10062527157973118 1.9524969294216505 -0.11054733295177119 1.9896790370696138 -0.12144774996275745 2.027554574640975 -0.13342299246107803 2.066135911854209 -0.1465790426148518 2.105435617488003 -0.16103233286537352 2.1454664617446606 -0.17691077636658686 2.186241418606926 -0.1943548990300838 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+946.6418604313682 9.794716279123387 +1041.0372349969568 9.962176946570759 +1144.845342203924 10.132179104372923 +1259.0047824464705 10.304750285998384 +1384.5477496302233 10.479917940598023 +1522.6093639462579 10.657709416967041 +1674.4379352723602 10.838151947029068 +1841.4062500000002 11.021272628840693 diff --git a/benchmark/RustQC/small/dupradar/test_expressionHist.png b/benchmark/RustQC/small/dupradar/test_expressionHist.png index 37dc3dd..b69c89c 100644 Binary files a/benchmark/RustQC/small/dupradar/test_expressionHist.png and b/benchmark/RustQC/small/dupradar/test_expressionHist.png differ diff --git a/benchmark/RustQC/small/dupradar/test_expressionHist.svg b/benchmark/RustQC/small/dupradar/test_expressionHist.svg index d17b706..e94c983 100644 --- a/benchmark/RustQC/small/dupradar/test_expressionHist.svg +++ b/benchmark/RustQC/small/dupradar/test_expressionHist.svg @@ -14,198 +14,194 @@ reads per kilobase (RPK) 0 - -5 - - - + 10 - - -15 - - - + + 20 - - -25 + + +30 - + - -0.1 - - - + - - + + 1 - - + + - - + + 10 - - + + - - + + 100 - - + + - - + + 1000 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/benchmark/RustQC/small/dupradar/test_intercept_slope.txt b/benchmark/RustQC/small/dupradar/test_intercept_slope.txt index ca922ac..acf1e44 100644 --- a/benchmark/RustQC/small/dupradar/test_intercept_slope.txt +++ b/benchmark/RustQC/small/dupradar/test_intercept_slope.txt @@ -1,2 +1,2 @@ -intercept 0.031858934078430205 -slope 1.6018851318110927 +intercept 0.027975359216305267 +slope 1.5772444664824248 diff --git a/benchmark/RustQC/small/featurecounts/test.featureCounts.tsv b/benchmark/RustQC/small/featurecounts/test.featureCounts.tsv index 0012099..f1cc0b7 100644 --- a/benchmark/RustQC/small/featurecounts/test.featureCounts.tsv +++ b/benchmark/RustQC/small/featurecounts/test.featureCounts.tsv @@ -1,4 +1,4 @@ -# Program:RustQC v0.1.0; Command:"rustqc rna benchmark/input/small/test.bam --gtf benchmark/input/small/chr6.gtf.gz -s 0 -p -t 4 -o benchmark/RustQC/small/" +# Program:RustQC v0.1.0; Command:"rustqc rna /Users/ewels/GitHub/seqera/RustQC/benchmark/input/small/test.bam --gtf /Users/ewels/GitHub/seqera/RustQC/benchmark/input/small/chr6.gtf.gz -s 0 -t 4 -o /tmp/rustqc_small_run --biotype-attribute gene_type --skip-dup-check" Geneid Chr Start End Strand Length test.bam ENSG00000271530 6 95124 95454 + 331 0 ENSG00000220212 6 105919 106856 - 938 0 diff --git a/benchmark/RustQC/small/preseq/test.lc_extrap.txt b/benchmark/RustQC/small/preseq/test.lc_extrap.txt index 4f9f0cf..8020456 100644 --- a/benchmark/RustQC/small/preseq/test.lc_extrap.txt +++ b/benchmark/RustQC/small/preseq/test.lc_extrap.txt @@ -1,10002 +1,10002 @@ TOTAL_READS EXPECTED_DISTINCT LOWER_0.95CI UPPER_0.95CI 0.0 0.0 0.0 0.0 -1000000.0 609060.3 537793.9 870344.6 -2000000.0 892742.1 739074.7 1245776.2 -3000000.0 1055425.2 844557.6 1588870.1 -4000000.0 1160705.9 909448.6 1847062.5 -5000000.0 1226993.5 952854.4 1837029.4 -6000000.0 1281244.5 984560.1 1967784.0 -7000000.0 1323030.3 1008529.6 2073248.4 -8000000.0 1356204.4 1027286.5 2160114.9 -9000000.0 1383180.2 1042364.3 2232905.1 -10000000.0 1405546.5 1054748.9 2294784.9 -11000000.0 1424391.8 1065102.7 2348036.5 -12000000.0 1440486.9 1073887.3 2394347.1 -13000000.0 1454392.7 1081434.3 2434991.0 -14000000.0 1466527.7 1087988.2 2470948.4 -15000000.0 1477209.7 1093732.7 2502985.8 -16000000.0 1486685.0 1098809.1 2531711.0 -17000000.0 1495147.1 1103327.6 2557612.6 -18000000.0 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138.17026491923144 +87.0 131.73791225814335 +88.0 126.52430538390813 +89.0 124.93826090477395 +90.0 118.99773355368376 +91.0 106.52089075049993 +92.0 98.28753922727378 +93.0 94.29584133512684 +94.0 86.41234638111173 +95.0 73.35539511102925 +96.0 47.380321386719345 +97.0 35.25408830314463 +98.0 20.462144967463637 +99.0 2.868035973602601 diff --git a/benchmark/RustQC/small/qualimap/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt b/benchmark/RustQC/small/qualimap/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt new file mode 100644 index 0000000..4f4b7c5 --- /dev/null +++ b/benchmark/RustQC/small/qualimap/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt @@ -0,0 +1,101 @@ +#Transcript position Transcript coverage profile +0.0 0.45985873419909556 +1.0 0.4042260264404628 +2.0 0.35273159793287984 +3.0 0.3671858713588195 +4.0 0.44226146223538687 +5.0 0.4285845877887321 +6.0 0.5459898074999628 +7.0 0.6188552365315342 +8.0 0.6594146188115597 +9.0 0.6219606175453176 +10.0 0.6390773152421452 +11.0 0.5462858480546852 +12.0 0.5478151853789882 +13.0 0.5706280178579191 +14.0 0.6261004970347565 +15.0 0.5555764891910384 +16.0 0.5142882071730439 +17.0 0.5753341237940756 +18.0 0.5913445128483436 +19.0 0.5378686596381498 +20.0 0.5365677657723906 +21.0 0.5264146631466311 +22.0 0.5223013394521621 +23.0 0.5489226302249444 +24.0 0.5623393427418908 +25.0 0.5448771316805692 +26.0 0.5905033279970532 +27.0 0.6283152324438808 +28.0 0.5757263699016992 +29.0 0.5514441145142508 +30.0 0.5704461494916677 +31.0 0.5292552179039716 +32.0 0.4248813412532739 +33.0 0.3998683585608325 +34.0 0.4053834032618593 +35.0 0.3948529352632956 +36.0 0.3388529097724589 +37.0 0.38883819761819777 +38.0 0.37291980684116927 +39.0 0.30551253266889566 +40.0 0.31356111050074215 +41.0 0.36102670037431495 +42.0 0.44729716742583187 +43.0 0.516149312238174 +44.0 0.48034101363367826 +45.0 0.4186089704644462 +46.0 0.38711181216315016 +47.0 0.36788159494730915 +48.0 0.44639226368869805 +49.0 0.4844390145973733 +50.0 0.40622554936737487 +51.0 0.3846911903911039 +52.0 0.37132447129066926 +53.0 0.3890825360316024 +54.0 0.44004213695881894 +55.0 0.42096439578805034 +56.0 0.44343771142834787 +57.0 0.3672536297344288 +58.0 0.3984783545751608 +59.0 0.36135451331348845 +60.0 0.340526555941258 +61.0 0.38430123838567803 +62.0 0.44582198110893106 +63.0 0.4594623445206448 +64.0 0.3747858407585976 +65.0 0.3730148297196772 +66.0 0.42481471343903154 +67.0 0.43085705648401834 +68.0 0.38267324214070475 +69.0 0.35190212398897214 +70.0 0.40533414148698904 +71.0 0.48327943551422464 +72.0 0.45545942566631875 +73.0 0.44145659829383666 +74.0 0.3977790171210289 +75.0 0.3607566230328528 +76.0 0.4096061357901964 +77.0 0.5273047122405546 +78.0 0.6533038611370513 +79.0 0.7011642354297244 +80.0 0.7026384371256685 +81.0 0.6352243443548419 +82.0 0.5560066510059941 +83.0 0.47187530619505097 +84.0 0.5626608681867893 +85.0 0.6744274443406112 +86.0 0.686548103329224 +87.0 0.7602449283557768 +88.0 0.6965668638465421 +89.0 0.6282164153491886 +90.0 0.7022644328404811 +91.0 0.7039207879398276 +92.0 0.697652518927596 +93.0 0.6861103391550099 +94.0 0.5727774345541383 +95.0 0.48740887789007575 +96.0 0.48030793983351 +97.0 0.40422614642832067 +98.0 0.294333968940313 +99.0 0.08377780028706842 diff --git a/benchmark/RustQC/small/qualimap/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt b/benchmark/RustQC/small/qualimap/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt new file mode 100644 index 0000000..8eb0723 --- /dev/null +++ b/benchmark/RustQC/small/qualimap/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt @@ -0,0 +1,101 @@ +#Transcript position Transcript coverage profile +0.0 147.84709742275342 +1.0 152.92208574864313 +2.0 160.03408767950893 +3.0 156.24317349156163 +4.0 152.77536912216908 +5.0 159.46847520273354 +6.0 165.48909984803083 +7.0 169.30591784693053 +8.0 169.37610917096063 +9.0 169.90148628902674 +10.0 171.47508847672088 +11.0 175.76247492398664 +12.0 177.64429826425655 +13.0 184.2693208026291 +14.0 186.18682866488803 +15.0 186.17660772716826 +16.0 183.2137397314332 +17.0 175.07433265088008 +18.0 173.09685040448718 +19.0 177.99845829644607 +20.0 182.14832769525032 +21.0 179.9402821536317 +22.0 178.67619937760733 +23.0 177.73753207934672 +24.0 187.40437489977 +25.0 192.66032006707763 +26.0 195.13466622560358 +27.0 196.76627060106586 +28.0 199.0197775347085 +29.0 199.58679337765793 +30.0 197.39852570361566 +31.0 196.6060349287446 +32.0 199.82489106491386 +33.0 204.4633852358212 +34.0 203.32030609789817 +35.0 202.28878562552777 +36.0 202.558520874418 +37.0 207.14027099758823 +38.0 208.66003452398851 +39.0 212.20491575335083 +40.0 218.73090335820353 +41.0 217.6830072593792 +42.0 217.98191659565742 +43.0 214.40562276068422 +44.0 222.25959676976845 +45.0 219.73371145369848 +46.0 211.73844836299665 +47.0 200.57053430328781 +48.0 204.24083067893136 +49.0 207.89072765873215 +50.0 204.76217421934075 +51.0 203.90250650642656 +52.0 198.78987836344382 +53.0 196.18360919631547 +54.0 193.76426109005632 +55.0 184.90294944799942 +56.0 183.39896641169696 +57.0 179.67517804766794 +58.0 186.98928599896763 +59.0 191.44559596768187 +60.0 196.02041680739006 +61.0 198.5118459935298 +62.0 203.7465631372821 +63.0 202.99392517282837 +64.0 202.53399002435296 +65.0 198.62849194652478 +66.0 193.15309200151296 +67.0 190.07254201785878 +68.0 186.69358748172317 +69.0 186.7206096210839 +70.0 183.27784350674816 +71.0 184.135650589742 +72.0 184.892966811831 +73.0 181.07932883462115 +74.0 179.4426694318368 +75.0 174.50128117781097 +76.0 173.90577450696154 +77.0 174.58095200681677 +78.0 169.2147799320891 +79.0 165.10591291754494 +80.0 168.12706789473322 +81.0 173.09731424175652 +82.0 175.81640258682012 +83.0 177.79477282711252 +84.0 177.25487314002424 +85.0 176.73592482946876 +86.0 175.77662406577699 +87.0 169.06796078763688 +88.0 163.3223442270193 +89.0 160.36541075436082 +90.0 152.9136183436231 +91.0 138.15854683413662 +92.0 126.89110290565445 +93.0 120.20287641620895 +94.0 109.98646651736475 +95.0 94.48414786501688 +96.0 64.7853187712476 +97.0 49.02395842741694 +98.0 30.20274178495928 +99.0 6.217751342263061 diff --git a/benchmark/RustQC/small/qualimap/rnaseq_qc_results.txt b/benchmark/RustQC/small/qualimap/rnaseq_qc_results.txt index f57e5a7..3500e61 100644 --- a/benchmark/RustQC/small/qualimap/rnaseq_qc_results.txt +++ b/benchmark/RustQC/small/qualimap/rnaseq_qc_results.txt @@ -1,26 +1,57 @@ +RNA-Seq QC report +----------------------------------- + >>>>>>> Input - bam file = test + bam file = benchmark/input/small/test.bam + gff file = benchmark/input/small/chr6.gtf + counting algorithm = uniquely-mapped-reads + protocol = strand-specific-reverse + 5'-3' bias region size = 100 + 5'-3' bias number of top transcripts = 1000 + >>>>>>> Reads alignment - reads aligned = 49,573 - total alignments = 52,839 - secondary alignments = 3,266 - non-unique alignments = 3,266 - aligned to genes = 22,788 - ambiguous alignments = 2,392 - no feature assigned = 1,225 + reads aligned (left/right) = 24,797 / 24,776 + read pairs aligned = 24,773 + total alignments = 52,839 + secondary alignments = 3,266 + non-unique alignments = 5,496 + aligned to genes = 31,654 + ambiguous alignments = 1,054 + no feature assigned = 14,635 + not aligned = 0 + >>>>>>> Reads genomic origin - exonic = 3,004,919 (90.08%) - intronic = 161,566 (4.84%) - intergenic = 169,326 (5.08%) - overlapping exon = 10,938 (48.00%) + exonic = 31,654 (68.38%) + intronic = 13,689 (29.57%) + intergenic = 946 (2.04%) + overlapping exon = 5,748 (12.42%) + >>>>>>> Transcript coverage profile - 5' bias = 0.75 - 3' bias = 0.61 - 5'-3' bias = 1.14 + 5' bias = 0.71 + 3' bias = 0.57 + 5'-3' bias = 1.19 + + +>>>>>>> Junction analysis + + reads at junctions = 28,125 + + ACCT : 10.93% + AGGT : 6.67% + ATCT : 4.55% + GCCT : 4.22% + AGGG : 3.80% + AGAA : 2.90% + ACCC : 2.56% + GGCT : 2.54% + TCCT : 2.50% + ACCA : 2.19% + TGTC : 2.18% + diff --git a/benchmark/RustQC/small/rseqc/inner_distance/test.inner_distance_plot.r b/benchmark/RustQC/small/rseqc/inner_distance/test.inner_distance_plot.r index fa658ed..646f9fe 100644 --- a/benchmark/RustQC/small/rseqc/inner_distance/test.inner_distance_plot.r +++ b/benchmark/RustQC/small/rseqc/inner_distance/test.inner_distance_plot.r @@ -1,5 +1,5 @@ -out_file = 'benchmark/RustQC/small/rseqc/inner_distance/test' -pdf('benchmark/RustQC/small/rseqc/inner_distance/test.inner_distance_plot.pdf') +out_file = '/tmp/rustqc_small_run/rseqc/inner_distance/test' +pdf('/tmp/rustqc_small_run/rseqc/inner_distance/test.inner_distance_plot.pdf') fragsize=rep(c(-247.5,-242.5,-237.5,-232.5,-227.5,-222.5,-217.5,-212.5,-207.5,-202.5,-197.5,-192.5,-187.5,-182.5,-177.5,-172.5,-167.5,-162.5,-157.5,-152.5,-147.5,-142.5,-137.5,-132.5,-127.5,-122.5,-117.5,-112.5,-107.5,-102.5,-97.5,-92.5,-87.5,-82.5,-77.5,-72.5,-67.5,-62.5,-57.5,-52.5,-47.5,-42.5,-37.5,-32.5,-27.5,-22.5,-17.5,-12.5,-7.5,-2.5,2.5,7.5,12.5,17.5,22.5,27.5,32.5,37.5,42.5,47.5,52.5,57.5,62.5,67.5,72.5,77.5,82.5,87.5,92.5,97.5,102.5,107.5,112.5,117.5,122.5,127.5,132.5,137.5,142.5,147.5,152.5,157.5,162.5,167.5,172.5,177.5,182.5,187.5,192.5,197.5,202.5,207.5,212.5,217.5,222.5,227.5,232.5,237.5,242.5,247.5),times=c(0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,11,424,624,1123,915,798,884,756,701,660,602,569,520,425,433,385,347,348,338,310,312,315,281,284,281,282,249,277,236,247,252,215,227,190,214,190,193,158,164,166,144,156,160,157,147,139,143,116,131,111,106,110,118,89,119,104,86,82,74,81,70,80,79,78,67,82,65,59,58,56,64,58,61,52,51,38,50,57,30,30)) frag_sd = sd(fragsize) frag_mean = mean(fragsize) diff --git a/benchmark/RustQC/small/rseqc/junction_annotation/test.junction_plot.r b/benchmark/RustQC/small/rseqc/junction_annotation/test.junction_plot.r index ca2978a..67634a6 100644 --- a/benchmark/RustQC/small/rseqc/junction_annotation/test.junction_plot.r +++ b/benchmark/RustQC/small/rseqc/junction_annotation/test.junction_plot.r @@ -1,8 +1,8 @@ -pdf("benchmark/RustQC/small/rseqc/junction_annotation/test.splice_events.pdf") +pdf("/tmp/rustqc_small_run/rseqc/junction_annotation/test.splice_events.pdf") events=c(0.708,2.790,96.502) pie(events,col=c(2,3,4),init.angle=30,angle=c(60,120,150),density=c(70,70,70),main="splicing events",labels=c("partial_novel 1%","complete_novel 3%","known 97%")) dev.off() -pdf("benchmark/RustQC/small/rseqc/junction_annotation/test.splice_junction.pdf") +pdf("/tmp/rustqc_small_run/rseqc/junction_annotation/test.splice_junction.pdf") junction=c(2.699,5.857,91.444) pie(junction,col=c(2,3,4),init.angle=30,angle=c(60,120,150),density=c(70,70,70),main="splicing junctions",labels=c("partial_novel 3%","complete_novel 6%","known 91%")) dev.off() diff --git a/benchmark/RustQC/small/rseqc/junction_saturation/test.junctionSaturation_plot.r b/benchmark/RustQC/small/rseqc/junction_saturation/test.junctionSaturation_plot.r index 6eff0f6..50a1d29 100644 --- a/benchmark/RustQC/small/rseqc/junction_saturation/test.junctionSaturation_plot.r +++ b/benchmark/RustQC/small/rseqc/junction_saturation/test.junctionSaturation_plot.r @@ -1,4 +1,4 @@ -pdf('benchmark/RustQC/small/rseqc/junction_saturation/test.junctionSaturation_plot.pdf') +pdf('/tmp/rustqc_small_run/rseqc/junction_saturation/test.junctionSaturation_plot.pdf') x=c(5,10,15,20,25,30,35,40,45,50,55,60,65,70,75,80,85,90,95,100) y=c(534,865,1136,1360,1550,1723,1873,1996,2117,2240,2341,2430,2507,2586,2655,2720,2774,2833,2887,2944) z=c(576,931,1212,1461,1663,1851,2019,2159,2293,2429,2541,2648,2739,2834,2918,2996,3056,3126,3193,3261) diff --git a/benchmark/RustQC/small/rseqc/tin/test.summary.txt b/benchmark/RustQC/small/rseqc/tin/test.summary.txt index faa9d71..4b761cd 100644 --- a/benchmark/RustQC/small/rseqc/tin/test.summary.txt +++ b/benchmark/RustQC/small/rseqc/tin/test.summary.txt @@ -1,2 +1,2 @@ Bam_file TIN(mean) TIN(median) TIN(stdev) -benchmark/input/small/test.bam 85.22 86.78 8.46 +/Users/ewels/GitHub/seqera/RustQC/benchmark/input/small/test.bam 85.22 86.78 8.46 diff --git a/benchmark/RustQC/small/samtools/test.stats b/benchmark/RustQC/small/samtools/test.stats index f45707a..7489fd8 100644 --- a/benchmark/RustQC/small/samtools/test.stats +++ b/benchmark/RustQC/small/samtools/test.stats @@ -12,7 +12,7 @@ SN reads unmapped: 0 SN reads properly paired: 49546 # proper-pair bit set SN reads paired: 49573 # paired-end technology bit set SN reads duplicated: 6097 # PCR or optical duplicate bit set -SN reads MQ0: 42 # mapped and MQ=0 +SN reads MQ0: 230 # mapped and MQ=0 SN reads QC failed: 0 SN non-primary alignments: 3266 SN supplementary alignments: 0 @@ -32,8 +32,8 @@ SN maximum length: 151 SN maximum first fragment length: 151 SN maximum last fragment length: 151 SN average quality: 38.6 -SN insert size average: 5771.6 -SN insert size standard deviation: 29364.0 +SN insert size average: 2202.4 +SN insert size standard deviation: 6314.5 SN inward oriented pairs: 23385 SN outward oriented pairs: 1388 SN pairs with other orientation: 0 diff --git a/benchmark/qualimap/large/images_qualimapReport/Coverage Profile Along Genes (High).png b/benchmark/qualimap/large/images_qualimapReport/Coverage Profile Along Genes (High).png index 1eefa08..9b39afb 100644 Binary files a/benchmark/qualimap/large/images_qualimapReport/Coverage Profile Along Genes (High).png and b/benchmark/qualimap/large/images_qualimapReport/Coverage Profile Along Genes (High).png differ diff --git a/benchmark/qualimap/large/images_qualimapReport/Coverage Profile Along Genes (Low).png b/benchmark/qualimap/large/images_qualimapReport/Coverage Profile Along Genes (Low).png index 1a1f3cb..e04a7fb 100644 Binary files a/benchmark/qualimap/large/images_qualimapReport/Coverage Profile Along Genes (Low).png and b/benchmark/qualimap/large/images_qualimapReport/Coverage Profile Along Genes (Low).png differ diff --git a/benchmark/qualimap/large/images_qualimapReport/Coverage Profile Along Genes (Total).png b/benchmark/qualimap/large/images_qualimapReport/Coverage Profile Along Genes (Total).png index d35e281..8650603 100644 Binary files a/benchmark/qualimap/large/images_qualimapReport/Coverage Profile Along Genes (Total).png and b/benchmark/qualimap/large/images_qualimapReport/Coverage Profile Along Genes (Total).png differ diff --git a/benchmark/qualimap/large/images_qualimapReport/Junction Analysis.png b/benchmark/qualimap/large/images_qualimapReport/Junction Analysis.png index b7bce74..dd9033f 100644 Binary files a/benchmark/qualimap/large/images_qualimapReport/Junction Analysis.png and b/benchmark/qualimap/large/images_qualimapReport/Junction Analysis.png differ diff --git a/benchmark/qualimap/large/images_qualimapReport/Reads Genomic Origin.png b/benchmark/qualimap/large/images_qualimapReport/Reads Genomic Origin.png index da8db60..40acd23 100644 Binary files a/benchmark/qualimap/large/images_qualimapReport/Reads Genomic Origin.png and b/benchmark/qualimap/large/images_qualimapReport/Reads Genomic Origin.png differ diff --git a/benchmark/qualimap/large/images_qualimapReport/Transcript coverage histogram.png b/benchmark/qualimap/large/images_qualimapReport/Transcript coverage histogram.png index 774a619..a9e9e71 100644 Binary files a/benchmark/qualimap/large/images_qualimapReport/Transcript coverage histogram.png and b/benchmark/qualimap/large/images_qualimapReport/Transcript coverage histogram.png differ diff --git a/benchmark/qualimap/large/qualimapReport.html b/benchmark/qualimap/large/qualimapReport.html index 83e39d3..5f7daa8 100644 --- a/benchmark/qualimap/large/qualimapReport.html +++ b/benchmark/qualimap/large/qualimapReport.html @@ -32,11 +32,11 @@

Input

- + - + @@ -44,7 +44,7 @@

Input

- + @@ -60,11 +60,11 @@

Input

- + - +
Analysis date: Mon Feb 16 19:21:58 GMT 2026Tue Mar 03 16:33:02 GMT 2026
BAM file: /data/input/large/GM12878_REP1.markdup.sorted.bam/data/GM12878_REP1.namesorted.bam
Counting algorithm:
GTF file: /data/input/large/genes.nochr.gtf/data/genes.filtered.gtf
Number of bases for 5'-3' bias computation:
Protocol: non-strand-specificstrand-specific-reverse
Sorting performed:yesno
@@ -102,24 +102,20 @@

Reads alignment

Aligned to genes: -15,615,099 +126,404,800 Ambiguous alignments: -332,227 +2,552,785 No feature assigned: -152,048,024 +39,037,765 Not aligned: 0 - -Strand specificity estimation (fwd/rev): -0.28 / 0.72 - @@ -129,19 +125,19 @@

Reads genomic origin

- + - + - + - +
Exonic: 15,615,099 / 9.31%126,404,800 / 76.4%
Intronic: 105,144,042 / 62.71%30,407,985 / 18.38%
Intergenic: 46,903,982 / 27.98%8,629,780 / 5.22%
Intronic/intergenic overlapping exon: 6,951,294 / 4.15%6,853,516 / 4.14%
@@ -152,15 +148,15 @@

Transcript coverage profile

- + - + - +
5' bias:0.310.87
3' bias:0.220.78
5'-3' bias:1.471.11
@@ -310,7 +306,7 @@

Contents

-2026/02/16 19:22:04 +2026/03/03 16:33:06
diff --git a/benchmark/qualimap/large/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt b/benchmark/qualimap/large/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt index ae8d336..2c1ac2b 100644 --- a/benchmark/qualimap/large/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt +++ b/benchmark/qualimap/large/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt @@ -1,101 +1,101 @@ #Transcript position Transcript coverage profile -0.0 8883.564356363036 -1.0 11163.163746182052 -2.0 12973.34525317428 -3.0 15296.573134340011 -4.0 17572.814790900273 -5.0 21038.655372128247 -6.0 22705.61426472885 -7.0 21976.85631829613 -8.0 22480.62011468247 -9.0 22280.541351810763 -10.0 23585.97777632638 -11.0 25486.71309299409 -12.0 26591.522879608736 -13.0 27307.918257138652 -14.0 28096.9237083289 -15.0 28247.46584338771 -16.0 27511.46787093374 -17.0 26516.49154109914 -18.0 26580.41016178216 -19.0 29084.180058014746 -20.0 29866.291110684033 -21.0 29724.404016311484 -22.0 30573.04395021893 -23.0 30188.693591244006 -24.0 29094.653577188765 -25.0 27842.32551084077 -26.0 26542.23696264481 -27.0 26214.552104897317 -28.0 26829.71013417707 -29.0 28152.085164354023 -30.0 28160.908659408786 -31.0 27359.028417139332 -32.0 28334.31234167063 -33.0 28439.850885578242 -34.0 28846.49020525632 -35.0 27396.989528881815 -36.0 28654.94483951536 -37.0 28437.307171848457 -38.0 27557.46115077713 -39.0 26492.638828831212 -40.0 26514.149232580283 -41.0 26541.12515521889 -42.0 26581.02086851533 -43.0 26654.506066088205 -44.0 27346.131345140162 -45.0 28924.442279666808 -46.0 30806.285102739006 -47.0 30444.76361192385 -48.0 29446.1282733177 -49.0 29137.810900121916 -50.0 28778.669011924194 -51.0 27920.00106448283 -52.0 27165.034576279373 -53.0 26684.528685392015 -54.0 26777.52873277622 -55.0 28368.53756285713 -56.0 29347.079155234733 -57.0 29567.68140938246 -58.0 29702.497426392467 -59.0 29686.994156941822 -60.0 28988.712122918118 -61.0 29548.36502725872 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671869.8468221311 +40.0 678628.021067749 +41.0 675812.9182358639 +42.0 673430.1499388263 +43.0 671560.8019744516 +44.0 668991.4744220059 +45.0 666467.7476206151 +46.0 665168.2993600307 +47.0 661934.8881370308 +48.0 661003.6688885886 +49.0 657958.5647893761 +50.0 655024.0763922152 +51.0 654895.3568533171 +52.0 652588.3306102622 +53.0 650896.3015667743 +54.0 648889.8430653432 +55.0 646309.4664504811 +56.0 637806.3169033194 +57.0 630874.3848977289 +58.0 628723.2376096557 +59.0 628482.1846948537 +60.0 623880.0129043172 +61.0 619248.9394724689 +62.0 618802.6259374759 +63.0 619332.3383574806 +64.0 614028.1561304714 +65.0 607403.8388743975 +66.0 603894.535073459 +67.0 604821.8569119538 +68.0 605161.7906786192 +69.0 600108.145857918 +70.0 598374.634056547 +71.0 594551.2237388071 +72.0 591218.5610478773 +73.0 588336.616287302 +74.0 580917.1662146776 +75.0 576432.816054172 +76.0 571549.2628044785 +77.0 566282.2419053244 +78.0 560809.6773539715 +79.0 558504.6315925795 +80.0 554492.5775871263 +81.0 550091.813781998 +82.0 544105.3297481805 +83.0 540211.9818949645 +84.0 531158.571214608 +85.0 523666.9075757544 +86.0 511002.0863837515 +87.0 498437.346894017 +88.0 479324.76192941243 +89.0 457861.4442267316 +90.0 430154.229445751 +91.0 396059.8902836792 +92.0 361701.6549649779 +93.0 319105.3923743566 +94.0 278565.1979848222 +95.0 234499.09268463237 +96.0 181229.624517191 +97.0 129163.80931557395 +98.0 78266.65990815204 +99.0 24459.03392057976 diff --git a/benchmark/qualimap/large/rnaseq_qc_results.txt b/benchmark/qualimap/large/rnaseq_qc_results.txt index 34c8bf6..bfc3d34 100644 --- a/benchmark/qualimap/large/rnaseq_qc_results.txt +++ b/benchmark/qualimap/large/rnaseq_qc_results.txt @@ -3,10 +3,10 @@ RNA-Seq QC report >>>>>>> Input - bam file = /data/input/large/GM12878_REP1.markdup.sorted.bam - gff file = /data/input/large/genes.nochr.gtf + bam file = /data/GM12878_REP1.namesorted.bam + gff file = /data/genes.filtered.gtf counting algorithm = uniquely-mapped-reads - protocol = non-strand-specific + protocol = strand-specific-reverse 5'-3' bias region size = 100 5'-3' bias number of top transcripts = 1000 @@ -18,26 +18,25 @@ RNA-Seq QC report total alignments = 185,718,543 secondary alignments = 10,620,822 non-unique alignments = 17,723,193 - aligned to genes = 15,615,099 - ambiguous alignments = 332,227 - no feature assigned = 152,048,024 + aligned to genes = 126,404,800 + ambiguous alignments = 2,552,785 + no feature assigned = 39,037,765 not aligned = 0 - SSP estimation (fwd/rev) = 0.28 / 0.72 >>>>>>> Reads genomic origin - exonic = 15,615,099 (9.31%) - intronic = 105,144,042 (62.71%) - intergenic = 46,903,982 (27.98%) - overlapping exon = 6,951,294 (4.15%) + exonic = 126,404,800 (76.4%) + intronic = 30,407,985 (18.38%) + intergenic = 8,629,780 (5.22%) + overlapping exon = 6,853,516 (4.14%) >>>>>>> Transcript coverage profile - 5' bias = 0.31 - 3' bias = 0.22 - 5'-3' bias = 1.47 + 5' bias = 0.87 + 3' bias = 0.78 + 5'-3' bias = 1.11 >>>>>>> Junction analysis diff --git a/benchmark/qualimap/small/rnaseq_qc_results.txt b/benchmark/qualimap/small/rnaseq_qc_results.txt index 718c7d9..ef8cf9a 100644 --- a/benchmark/qualimap/small/rnaseq_qc_results.txt +++ b/benchmark/qualimap/small/rnaseq_qc_results.txt @@ -3,10 +3,10 @@ RNA-Seq QC report >>>>>>> Input - bam file = /data/input/small/test.bam - gff file = /data/input/small/chr6.gtf + bam file = /tmp/rustqc_bench/test.namesorted.bam + gff file = /data/chr6.gtf counting algorithm = uniquely-mapped-reads - protocol = non-strand-specific + protocol = strand-specific-reverse 5'-3' bias region size = 100 5'-3' bias number of top transcripts = 1000 @@ -18,19 +18,18 @@ RNA-Seq QC report total alignments = 52,839 secondary alignments = 3,266 non-unique alignments = 5,496 - aligned to genes = 31,136 - ambiguous alignments = 1,754 - no feature assigned = 14,453 + aligned to genes = 31,654 + ambiguous alignments = 1,054 + no feature assigned = 14,635 not aligned = 0 - SSP estimation (fwd/rev) = 0.03 / 0.97 >>>>>>> Reads genomic origin - exonic = 31,136 (68.3%) - intronic = 13,537 (29.69%) - intergenic = 916 (2.01%) - overlapping exon = 5,748 (12.61%) + exonic = 31,654 (68.38%) + intronic = 13,689 (29.57%) + intergenic = 946 (2.04%) + overlapping exon = 5,748 (12.42%) >>>>>>> Transcript coverage profile diff --git a/docs/astro.config.mjs b/docs/astro.config.mjs index 79ab79d..215f4ae 100644 --- a/docs/astro.config.mjs +++ b/docs/astro.config.mjs @@ -50,7 +50,8 @@ export default defineConfig({ { label: "dupRadar", slug: "outputs/dupradar" }, { label: "featureCounts", slug: "outputs/featurecounts" }, { label: "RSeQC", slug: "outputs/rseqc" }, - { label: "TIN & Gene Body", slug: "outputs/tin" }, + { label: "TIN", slug: "outputs/tin" }, + { label: "Qualimap", slug: "outputs/qualimap" }, { label: "preseq", slug: "outputs/preseq" }, { label: "Samtools", slug: "outputs/samtools" }, ], @@ -62,6 +63,7 @@ export default defineConfig({ { label: "dupRadar", slug: "benchmarks/dupradar" }, { label: "featureCounts", slug: "benchmarks/featurecounts" }, { label: "RSeQC", slug: "benchmarks/rseqc" }, + { label: "Qualimap", slug: "benchmarks/qualimap" }, { label: "preseq", slug: "benchmarks/preseq" }, { label: "Samtools", slug: "benchmarks/samtools" }, ], diff --git a/docs/src/content/docs/benchmarks/combined.md b/docs/src/content/docs/benchmarks/combined.md index 5375db9..ab7659c 100644 --- a/docs/src/content/docs/benchmarks/combined.md +++ b/docs/src/content/docs/benchmarks/combined.md @@ -34,10 +34,11 @@ to GRCh38 (63,086 genes). | samtools idxstats | <1s | -- | | samtools stats | ~5m | -- | | preseq lc_extrap | ~3m | -- | +| samtools sort -n (for Qualimap) | ~5-10m | -- | | Qualimap rnaseq | ~10m | -- | | Biotype summaries | Additional scripting | -- | | **All outputs, single pass** | -- | **~5m** | -| **Total** | **~2h 5m** | **~5m** | +| **Total** | **~2h 15m** | **~5m** | RustQC produces all outputs -- dupRadar duplication matrix, model fit, plots, featureCounts-compatible counts, assignment summary, biotype counts, all 7 @@ -72,10 +73,12 @@ Every output file produced by RustQC matches the original tools: - **stats** core SN metrics (read counts, lengths, duplicates) match samtools stats - **preseq** extrapolation curve within <0.1% of preseq v3.2.0 across entire range - **RSeQC tools** all values match Python RSeQC (see [RSeQC benchmark](rseqc/)) +- **Qualimap** all read counts, genomic origin percentages, and coverage bias metrics + match Qualimap Java 2.3 exactly (see [Qualimap benchmark](qualimap/)) See the individual benchmark pages for detailed per-tool comparisons: [dupRadar](dupradar/), [featureCounts](featurecounts/), [RSeQC](rseqc/), -[preseq](preseq/), [Samtools](samtools/). +[preseq](preseq/), [Samtools](samtools/), [Qualimap](qualimap/). ## Benchmark conditions diff --git a/docs/src/content/docs/benchmarks/qualimap.mdx b/docs/src/content/docs/benchmarks/qualimap.mdx new file mode 100644 index 0000000..b6137db --- /dev/null +++ b/docs/src/content/docs/benchmarks/qualimap.mdx @@ -0,0 +1,105 @@ +--- +title: Qualimap Benchmarks +description: Benchmark comparison of RustQC's Qualimap rnaseq output against the original Qualimap Java implementation. +--- + +## Performance + +RustQC's Qualimap analysis runs in the same single-pass BAM scan as all other +tools, adding negligible overhead to the total runtime. The original Qualimap +Java implementation requires a separate dedicated run on a **name-sorted** BAM +file, meaning a `samtools sort -n` step is typically needed before Qualimap can +run. RustQC works directly on coordinate-sorted BAMs (the standard output of +most aligners), eliminating that preprocessing step entirely. + +| Tool | Runtime | Notes | +|------|---------|-------| +| `samtools sort -n` | ~5-10 min | Name-sort required by Qualimap Java (not needed by RustQC) | +| Qualimap rnaseq (Java) | ~10 min | Separate BAM pass, single-threaded, requires name-sorted input | +| RustQC (all tools) | ~4 min | Single pass, all analyses combined, coordinate-sorted input | + +In a typical pipeline, the original Qualimap workflow requires **15-20 minutes** +(name-sort + Qualimap), while RustQC produces identical output with **zero +additional cost** beyond its shared BAM scan. + +## Output comparison + +RustQC produces output identical to Qualimap Java across all key metrics. +Both tools were run on the same dataset with matching parameters +(`--stranded 2` / `strand-specific-reverse`, same GENCODE GTF). + +### Reads alignment + +| Metric | RustQC | Qualimap Java | Match? | +|--------|--------|---------------|--------| +| reads aligned (left/right) | 87,559,392 / 87,538,329 | 87,559,392 / 87,538,329 | ✅ | +| read pairs aligned | 87,420,177 | 87,420,177 | ✅ | +| total alignments | 185,718,543 | 185,718,543 | ✅ | +| secondary alignments | 10,620,822 | 10,620,822 | ✅ | +| non-unique alignments | 17,723,193 | 17,723,193 | ✅ | +| aligned to genes | 126,404,800 | 126,404,800 | ✅ | +| ambiguous alignments | 2,552,785 | 2,552,785 | ✅ | +| no feature assigned | 39,037,765 | 39,037,765 | ✅ | + +### Reads genomic origin + +| Metric | RustQC | Qualimap Java | Match? | +|--------|--------|---------------|--------| +| exonic | 126,404,800 (76.4%) | 126,404,800 (76.4%) | ✅ | +| intronic | 30,407,985 (18.38%) | 30,407,985 (18.38%) | ✅ | +| intergenic | 8,629,780 (5.22%) | 8,629,780 (5.22%) | ✅ | +| overlapping exon | 6,853,516 (4.14%) | 6,853,516 (4.14%) | ✅ | + +### Transcript coverage profile + +| Metric | RustQC | Qualimap Java | Match? | +|--------|--------|---------------|--------| +| 5' bias | 0.87 | 0.87 | ✅ | +| 3' bias | 0.78 | 0.78 | ✅ | +| 5'-3' bias | 1.11 | 1.11 | ✅ | + +RustQC produces a 100-bin coverage profile along normalized gene body positions +(5' to 3'), matching the format produced by Qualimap. Three tiers are generated: +total (all genes), high (top 500 by expression), and low (bottom 500). + +The high-expression tier coverage profile is an **exact numerical match** with +Qualimap Java. The total (all-genes) tier shows negligible floating-point +differences (<0.03% relative) due to coverage aggregation order. + +### Junction analysis + +| Metric | RustQC | Qualimap Java | Match? | +|--------|--------|---------------|--------| +| reads at junctions | 60,467,173 | 60,467,173 | ✅ | + +Junction motif frequencies match with minor percentage rounding differences +(e.g., ACCT 5.59% vs 5.55%). The underlying read counts are identical. + +### QC results file + +The `rnaseq_qc_results.txt` file is formatted identically to Qualimap's output +and is directly parseable by MultiQC's Qualimap rnaseq module, including: + +- **Reads alignment** -- primary alignments, secondary, multi-mappers, gene + assignment counts +- **Reads genomic origin** -- exonic, intronic, intergenic, and overlapping-exon + read counts with percentages +- **Transcript coverage profile** -- 5'/3' bias metrics +- **Junction analysis** -- junction read counts and motif frequencies + +### Implementation details + +RustQC replicates Qualimap's merged exon model (Picard Gene.Transcript) for +non-redundant per-gene coverage. This means overlapping exons from different +transcripts of the same gene are merged before computing coverage, avoiding +double-counting. The read enclosure check, strand-specificity estimation, and +junction motif counting all follow Qualimap's algorithms. + +## Benchmark conditions + +- **BAM file**: GM12878 ENCODE RNA-Seq, paired-end, ~185M reads, 10 GB +- **Annotation**: GENCODE v47 GTF (filtered to standard chromosomes, used for both tools) +- **Strandedness**: strand-specific-reverse (`--stranded 2` / `-p strand-specific-reverse`) +- **Qualimap version**: 2.3 (Java implementation, name-sorted BAM input) +- **RustQC**: 10 threads, `--gtf` mode, coordinate-sorted BAM input +- **Hardware**: Apple M3 Max, 128 GB RAM diff --git a/docs/src/content/docs/benchmarks/rseqc.mdx b/docs/src/content/docs/benchmarks/rseqc.mdx index ef3c8aa..6b3b8dc 100644 --- a/docs/src/content/docs/benchmarks/rseqc.mdx +++ b/docs/src/content/docs/benchmarks/rseqc.mdx @@ -219,27 +219,14 @@ provides a cleaner summary with one score per gene. ## Gene body coverage (Qualimap) -RustQC produces Qualimap-compatible gene body coverage output, including: -- A 100-bin coverage profile along normalized gene body positions (5' to 3') -- A Qualimap `rnaseq_qc_results.txt` file parseable by MultiQC - -### Coverage bias metrics - -| Metric | Value | -| --- | --- | -| 5' bias | 1.20 | -| 3' bias | 0.92 | -| 5'-3' bias | 1.24 | - -These metrics help identify degradation patterns — a 5'-3' bias significantly -above 1.0 may indicate RNA degradation, while values near 1.0 indicate -uniform coverage. +See the dedicated [Qualimap Benchmark](/benchmarks/qualimap/) page for gene +body coverage profiling, bias metrics, and Qualimap-compatible output comparison. ## Benchmark conditions - **BAM file**: GM12878 ENCODE RNA-Seq, paired-end, ~185M reads, 10 GB - **Annotation**: Ensembl BED12 gene model (same file used by both RSeQC and RustQC); - Ensembl GTF used for TIN and gene body coverage (require gene-level annotation) + Ensembl GTF used for TIN and Qualimap (require gene-level annotation) - **RSeQC version**: 5.0.4 (run via Docker on Apple M3 Max with Rosetta x86 emulation) -- **RustQC**: 10 threads, `--gtf` mode for TIN/genebody, `--bed` mode for RSeQC tools +- **RustQC**: 10 threads, `--gtf` mode for TIN/Qualimap, `--bed` mode for RSeQC tools - **Hardware**: Apple M3 Max, 128 GB RAM diff --git a/docs/src/content/docs/getting-started/introduction.md b/docs/src/content/docs/getting-started/introduction.md index 3e729eb..01c8512 100644 --- a/docs/src/content/docs/getting-started/introduction.md +++ b/docs/src/content/docs/getting-started/introduction.md @@ -45,7 +45,7 @@ Given a duplicate-marked BAM file and a GTF or BED12 annotation, `rustqc rna` ru 6. **Outputs featureCounts-format files** including biotype-level summaries 7. **Estimates library complexity** via extrapolation (preseq lc_extrap equivalent) 8. **Computes Transcript Integrity Number (TIN)** for RNA degradation assessment -9. **Profiles gene body coverage** with Qualimap-compatible output +9. **Runs Qualimap rnaseq analysis**: gene body coverage profiling, 5'/3' bias metrics, read origin classification, strand-specificity estimation, and junction analysis -- all with Qualimap-compatible MultiQC-parseable output 10. **Produces samtools-compatible outputs** (flagstat, idxstats, stats) ### RSeQC tools -- RNA-seq quality control @@ -67,13 +67,13 @@ Seven reimplementations of [RSeQC](https://rseqc.sourceforge.net/) tools, plus T | Tool | Equivalent | Description | |------|-----------|-------------| +| Qualimap rnaseq | [Qualimap](http://qualimap.conesalab.org/) rnaseq | Gene body coverage profiling, 5'/3' bias metrics, read origin classification (exonic/intronic/intergenic), strand-specificity estimation, and junction analysis. Qualimap-compatible output parseable by MultiQC. | | preseq | [preseq](http://smithlabresearch.org/software/preseq/) `lc_extrap` | Library complexity extrapolation with bootstrap confidence intervals | -| gene body coverage | [Qualimap](http://qualimap.conesalab.org/) rnaseq | Coverage profile along gene bodies with 5'/3' bias metrics | | flagstat | `samtools flagstat` | Alignment flag statistics | | idxstats | `samtools idxstats` | Per-chromosome read counts | | stats | `samtools stats` | Summary number (SN) statistics | -When a GTF file is provided via `--gtf`, all tools run automatically — transcript-level structure is extracted from the GTF. Alternatively, a BED12 gene model file can be provided via `--bed` (mutually exclusive with `--gtf`), which runs the RSeQC tools, TIN, preseq, and samtools outputs, but skips dupRadar, featureCounts, and gene body coverage (they require a GTF). Both GTF and BED files can be provided plain or gzip-compressed (`.gz`) — compression is detected automatically. Individual tools can be disabled via the YAML configuration file. +When a GTF file is provided via `--gtf`, all tools run automatically — transcript-level structure is extracted from the GTF. Alternatively, a BED12 gene model file can be provided via `--bed` (mutually exclusive with `--gtf`), which runs the RSeQC tools, TIN, preseq, and samtools outputs, but skips dupRadar, featureCounts, and Qualimap (they require a GTF). Both GTF and BED files can be provided plain or gzip-compressed (`.gz`) — compression is detected automatically. Individual tools can be disabled via the YAML configuration file. ## Credits diff --git a/docs/src/content/docs/getting-started/quickstart.md b/docs/src/content/docs/getting-started/quickstart.md index f1bbba6..6a47f79 100644 --- a/docs/src/content/docs/getting-started/quickstart.md +++ b/docs/src/content/docs/getting-started/quickstart.md @@ -49,13 +49,14 @@ will find in the output directory: | `samtools/sample.markdup.idxstats` | samtools idxstats-compatible output | | `samtools/sample.markdup.stats` | samtools stats SN-compatible output | | `preseq/sample.markdup.lc_extrap.txt` | Library complexity extrapolation | -| `qualimap/rnaseq_qc_results.txt` | Qualimap-compatible QC summary | +| `qualimap/rnaseq_qc_results.txt` | Qualimap-compatible QC report (bias, read origin, SSP) | +| `qualimap/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt` | Gene body coverage profile | Plus SVG versions of all plots, biotype count tables, and MultiQC-compatible report files. Use `--flat-output` to write all files directly to the output directory without subdirectories. -See [dupRadar Outputs](/outputs/dupradar/), [featureCounts Outputs](/outputs/featurecounts/), [RSeQC Outputs](/outputs/rseqc/), [Preseq Outputs](/outputs/preseq/), [Samtools Outputs](/outputs/samtools/), and [TIN & Gene Body Coverage](/outputs/tin/) for full details. +See [dupRadar Outputs](/outputs/dupradar/), [featureCounts Outputs](/outputs/featurecounts/), [RSeQC Outputs](/outputs/rseqc/), [TIN](/outputs/tin/), [Qualimap](/outputs/qualimap/), [Preseq Outputs](/outputs/preseq/), and [Samtools Outputs](/outputs/samtools/) for full details. ## RSeQC quality control tools diff --git a/docs/src/content/docs/outputs/qualimap.mdx b/docs/src/content/docs/outputs/qualimap.mdx new file mode 100644 index 0000000..3eae23c --- /dev/null +++ b/docs/src/content/docs/outputs/qualimap.mdx @@ -0,0 +1,226 @@ +--- +title: Qualimap Outputs +description: Output files produced by RustQC's Qualimap rnaseq-compatible RNA-Seq quality control analysis. +--- + +import { FileTree } from '@astrojs/starlight/components'; + +## What is Qualimap? + +[Qualimap](http://qualimap.conesalab.org/) is a platform-independent application +for quality control of sequencing alignment data. RustQC reimplements the +**rnaseq mode** of Qualimap, producing identical output that is directly parseable +by [MultiQC](https://multiqc.info/). + +The Qualimap analysis runs automatically as part of `rustqc rna` in the same +single-pass BAM scan as all other analyses -- at negligible additional cost. + +### What it provides + +RustQC's Qualimap module computes: + +- **Gene body coverage profiles** -- coverage distribution along normalized + transcript positions from 5' to 3', revealing systematic biases such as 3' + degradation or incomplete reverse transcription +- **5'/3' bias metrics** -- quantitative measures of coverage uniformity across + gene bodies, used for sample QC and batch-effect detection +- **Read origin classification** -- counts reads as exonic, intronic, intergenic, + or overlapping multiple genes' exons +- **Strand-specificity estimation** -- validates whether the observed strand + distribution matches the expected library protocol +- **Splice junction motif analysis** -- counts canonical and non-canonical + donor/acceptor junction motifs across all uniquely-mapped reads +- **Alignment statistics** -- primary/secondary alignments, multi-mappers, + proper pairs, and supplementary read counts + +:::note +Qualimap analyses only run in GTF mode (`--gtf`). They are skipped when using +`--bed` because the merged exon models, transcript structure, and biotype +information needed for coverage profiling and read origin classification are +only available from GTF annotations. +::: + +## Output files + +All Qualimap output files are written to a `qualimap/` subdirectory under the +output directory, matching the directory structure that MultiQC expects. + + +- qualimap/ + - rnaseq_qc_results.txt Qualimap-compatible QC report + - raw_data_qualimapReport/ + - coverage_profile_along_genes_(total).txt Coverage profile -- all genes + - coverage_profile_along_genes_(high).txt Coverage profile -- highly expressed genes + - coverage_profile_along_genes_(low).txt Coverage profile -- lowly expressed genes + + +### QC results + +**File:** `rnaseq_qc_results.txt` + +The main QC report, formatted identically to Qualimap's rnaseq output. This +file is the primary input for MultiQC's Qualimap rnaseq module. It contains +four sections: + +#### Input + +``` +>>>>>>> Input + bam file = sample +``` + +#### Reads alignment + +Alignment-level statistics for all primary reads: + +``` +>>>>>>> Reads alignment + reads aligned (left/right) = 87,559,392 / 87,538,329 + read pairs aligned = 87,420,177 + total alignments = 185,718,543 + secondary alignments = 10,620,822 + non-unique alignments = 17,723,193 + aligned to genes = 126,404,800 + ambiguous alignments = 2,552,785 + no feature assigned = 39,037,765 + not aligned = 0 + SSP estimation (fwd/rev) = 0.04 / 0.96 +``` + +| Field | Description | +|-------|-------------| +| reads aligned | Total primary alignments (excluding secondary, supplementary, QC-fail) | +| total alignments | All mapped reads (primary + secondary) | +| secondary alignments | Alignments flagged as secondary (0x100) | +| non-unique alignments | Multi-mappers (NH tag > 1) | +| aligned to genes | Reads assigned to exactly one gene (exonic) | +| ambiguous alignments | Reads enclosed by multiple genes | +| no feature assigned | Reads with no enclosing gene annotation | +| not aligned | Unmapped reads encountered in the BAM | +| SSP estimation | Strand-specificity proportions (forward / reverse) | + +#### Reads genomic origin + +Per-base classification of read origin, counting each read's aligned bases +against the annotation: + +``` +>>>>>>> Reads genomic origin + exonic = 126,404,800 (76.4%) + intronic = 30,407,985 (18.38%) + intergenic = 8,629,780 (5.22%) + overlapping exon = 6,853,516 (4.14%) +``` + +| Field | Description | +|-------|-------------| +| exonic | Reads fully enclosed by a single gene's exons | +| intronic | Reads overlapping introns but not exons | +| intergenic | Reads in regions with no gene annotation | +| overlapping exon | Reads partially overlapping exons (not fully enclosed) | + +#### Transcript coverage profile + +Coverage bias metrics computed from the gene body coverage profile: + +``` +>>>>>>> Transcript coverage profile + 5' bias = 0.87 + 3' bias = 0.78 + 5'-3' bias = 1.11 +``` + +| Metric | Description | +|--------|-------------| +| 5' bias | Ratio of median coverage in the 5' region (first 100bp) to the median of the middle 80% | +| 3' bias | Ratio of median coverage in the 3' region (last 100bp) to the median of the middle 80% | +| 5'-3' bias | Ratio of 5' median to 3' median | + +Bias values close to 1.0 indicate uniform coverage. Values significantly above +1.0 for 5' bias or below 1.0 for 3' bias suggest degradation or protocol issues. + +### Coverage profiles + +**Files:** `coverage_profile_along_genes_(total|high|low).txt` + +Tab-separated files with 100 rows, one per percentile bin (0-99), showing the +normalized coverage depth at each position along the gene body: + +| Column | Description | +|--------|-------------| +| Position | Percentile position along gene body (0.0 to 99.0) | +| Coverage | Normalized coverage depth at this position | + +Three tiers are produced: + +| Tier | File | Description | +|------|------|-------------| +| Total | `coverage_profile_along_genes_(total).txt` | All expressed genes | +| High | `coverage_profile_along_genes_(high).txt` | Top 500 genes by mean coverage | +| Low | `coverage_profile_along_genes_(low).txt` | Bottom 500 genes by mean coverage | + +The **total** profile is the one parsed by MultiQC for the gene body coverage +plot. + +## Interpreting results + +### Gene body coverage shape + +| Pattern | Interpretation | +|---------|---------------| +| Flat/uniform | Good library quality -- even coverage across transcripts | +| 3' bias (rising right) | RNA degradation or oligo-dT priming bias | +| 5' bias (rising left) | Incomplete reverse transcription or random-priming protocol | +| Both-end dropout | Short fragment library or size-selection issue | + +### Bias metrics + +| Metric | Good | Problematic | +|--------|------|-------------| +| 5'-3' bias | 0.8 -- 1.2 | < 0.5 or > 2.0 | +| 5' bias | 0.8 -- 1.2 | > 2.0 (enrichment) or < 0.5 (depletion) | +| 3' bias | 0.8 -- 1.2 | > 2.0 (enrichment) or < 0.5 (depletion) | + +### Strand specificity + +For strand-specific libraries, one of the SSP values should be close to 1.0 +and the other close to 0.0. Common patterns: + +| Library type | Expected fwd | Expected rev | +|-------------|-------------|-------------| +| Unstranded | ~0.5 | ~0.5 | +| dUTP / Illumina TruSeq Stranded | ~0.02-0.05 | ~0.95-0.98 | +| Ligation (e.g. SMARTer) | ~0.95-0.98 | ~0.02-0.05 | + +## Configuration + +### YAML configuration + +```yaml +qualimap: + enabled: true # Whether to run the Qualimap analysis +``` + +When Qualimap is enabled (the default), the analysis runs in the same BAM pass +as dupRadar, featureCounts, and all other tools. The only additional requirement +is a GTF annotation file (`--gtf`). + +## Compatibility with Qualimap + +The output files are designed for direct parsing by MultiQC's Qualimap rnaseq +module. The directory structure (`qualimap/raw_data_qualimapReport/`) and file +formats match Qualimap's output. Key differences from the Java implementation: + +- **Single-pass**: RustQC computes Qualimap metrics alongside all other analyses + in one BAM scan, whereas the original requires a separate dedicated run +- **Merged exon model**: RustQC uses the same exon-merging strategy as Qualimap + (Picard Gene.Transcript model) for accurate non-redundant coverage +- **Multi-threading**: Coverage is accumulated per chromosome in parallel and + merged, producing identical results to the original's single-threaded approach + +## References + +- **Qualimap:** Garcia-Alcalde F, Okonechnikov K, Carbonell J, et al. Qualimap: + evaluating next-generation sequencing alignment data. *Bioinformatics*. + 2012;28(20):2678-2679. + [Qualimap website](http://qualimap.conesalab.org/) diff --git a/docs/src/content/docs/outputs/rseqc.mdx b/docs/src/content/docs/outputs/rseqc.mdx index e1f275f..28dfa1a 100644 --- a/docs/src/content/docs/outputs/rseqc.mdx +++ b/docs/src/content/docs/outputs/rseqc.mdx @@ -224,7 +224,7 @@ approximately normal for a well-prepared library. Measures transcript integrity via Shannon entropy of read coverage uniformity. A reimplementation of RSeQC's `tin.py` tool. For full details, see the -dedicated [TIN & Gene Body Coverage](/outputs/tin/) documentation page. +dedicated [TIN](/outputs/tin/) documentation page. | File | Description | |------|-------------| diff --git a/docs/src/content/docs/outputs/tin.mdx b/docs/src/content/docs/outputs/tin.mdx index a8f236b..450f9bb 100644 --- a/docs/src/content/docs/outputs/tin.mdx +++ b/docs/src/content/docs/outputs/tin.mdx @@ -1,27 +1,20 @@ --- -title: TIN & Gene Body Coverage Outputs -description: Output files produced by RustQC's TIN (Transcript Integrity Number) and gene body coverage analyses. +title: TIN Outputs +description: Output files produced by RustQC's TIN (Transcript Integrity Number) analysis. --- import { FileTree } from '@astrojs/starlight/components'; -RustQC includes two complementary RNA integrity analyses: +## What is TIN? -- **TIN (Transcript Integrity Number)** -- reimplementation of RSeQC's `tin.py`, - measuring transcript-level coverage uniformity via Shannon entropy -- **Gene body coverage** -- Qualimap-compatible output showing coverage distribution - along normalized gene body positions +TIN (Transcript Integrity Number) measures the **uniformity of read coverage** +across a transcript. A TIN score of 100 means perfectly uniform coverage; lower +scores indicate degradation or bias. TIN is computed using Shannon entropy of +read-start coverage at sampled positions along each transcript's exonic regions. -Both run automatically as part of `rustqc rna` in the same single-pass BAM scan. - -## TIN (Transcript Integrity Number) - -### What is TIN? - -TIN measures the **uniformity of read coverage** across a transcript. A TIN -score of 100 means perfectly uniform coverage; lower scores indicate degradation -or bias. TIN is computed using Shannon entropy of read-start coverage at sampled -positions along each transcript's exonic regions. +RustQC reimplements [RSeQC's `tin.py`](https://rseqc.sourceforge.net/#tin-py), +computing TIN scores automatically as part of `rustqc rna` in the same +single-pass BAM scan as all other analyses. TIN is particularly useful for: @@ -32,7 +25,7 @@ TIN is particularly useful for: - **Identifying problematic samples** -- samples with unusually low median TIN should be flagged for potential exclusion -### Output files +## Output files TIN output files use the BAM file stem as a prefix and are written to a `rseqc/tin/` subdirectory under the output directory. @@ -44,7 +37,7 @@ TIN output files use the BAM file stem as a prefix and are written to a - sample.summary.txt Summary statistics (mean, median, stdev) -#### TIN scores +### TIN scores **File:** `.tin.xls` @@ -71,7 +64,7 @@ ENSG00000268903.1 chr1 135140 135895 60.32 ENSG00000269981.1 chr1 137681 137965 85.89 ``` -#### Summary +### Summary **File:** `.summary.txt` @@ -91,7 +84,7 @@ Bam_file TIN(mean) TIN(median) TIN(stdev) sample.bam 72.55 83.89 26.14 ``` -### Interpreting TIN scores +## Interpreting TIN scores | Median TIN | Interpretation | |------------|---------------| @@ -104,7 +97,7 @@ A bimodal distribution of per-transcript TIN scores (some very high, some very low) can indicate selective degradation of certain transcript classes rather than global degradation. -### Configuration +## Configuration ```yaml tin: @@ -115,104 +108,13 @@ tin: TIN uses the shared `--mapq` / `-q` flag for mapping quality filtering. -## Gene body coverage - -### What is gene body coverage? - -Gene body coverage profiles show the distribution of read coverage along -normalized transcript positions from 5' to 3'. Each transcript is divided into -100 equal percentile bins, and coverage depth is accumulated across all -expressed genes. This reveals systematic biases such as: - -- **3' bias** -- typical of degraded RNA or oligo-dT primed libraries -- **5' bias** -- can indicate incomplete reverse transcription -- **Uniform coverage** -- ideal result, expected from high-quality libraries - -### Output files - -Gene body coverage output is written to a `qualimap/` subdirectory in a format -compatible with [Qualimap](http://qualimap.conesalab.org/) rnaseq output, which -[MultiQC](https://multiqc.info/) can parse directly. - - -- qualimap/ - - coverage_profile_along_genes_(total).txt Coverage profile (100 bins) - - rnaseq_qc_results.txt Qualimap-compatible QC summary - - -#### Coverage profile - -**File:** `coverage_profile_along_genes_(total).txt` - -A tab-separated file with 100 rows, one per percentile bin (0-99), showing the -cumulative coverage depth at each normalized position along the gene body: - -| Column | Description | -|--------|-------------| -| Position | Percentile position along gene body (0.0 to 99.0) | -| Coverage | Cumulative read depth at this position across all genes | - -#### QC results - -**File:** `rnaseq_qc_results.txt` - -A Qualimap rnaseq-compatible text file with four sections: - -- **Input** -- BAM file name -- **Reads alignment** -- total reads, alignments, secondary, aligned to genes, - ambiguous, no feature assigned -- **Reads genomic origin** -- exonic, intronic, and intergenic base counts with - percentages; overlapping exon count -- **Transcript coverage profile** -- 5' bias, 3' bias, and 5'-3' bias ratios - -Example: - -``` ->>>>>>> Input - bam file = sample - ->>>>>>> Reads alignment - reads aligned = 175,097,721 - total alignments = 185,718,543 - secondary alignments = 10,620,822 - ->>>>>>> Reads genomic origin - exonic = 744,941,713 (8.29%) - intronic = 837,462,849 (9.32%) - intergenic = 7,406,659,875 (82.40%) - ->>>>>>> Transcript coverage profile - 5' bias = 1.20 - 3' bias = 0.92 - 5'-3' bias = 1.24 -``` - -### Configuration - -```yaml -genebody_coverage: - enabled: true # Whether to produce gene body coverage output -``` - -Gene body coverage requires GTF annotation (`--gtf` mode) -- it is not -available in BED-only mode because it requires transcript-level exon structure -to normalize positions along the gene body. - ## Compatibility -### TIN - RustQC's TIN output uses the same file format and column names as RSeQC's `tin.py`. The key difference is that RustQC reports one row per **gene** (using the longest transcript as representative), while RSeQC reports one row per **transcript**. TIN scores are computed using the same Shannon entropy formula. -### Gene body coverage - -The Qualimap-compatible output files are designed for direct parsing by MultiQC's -Qualimap rnaseq module. The coverage profile format and QC results sections match -Qualimap's output structure. - ## References - **TIN:** Wang L, Nie J, Sicotte H, et al. Measure transcript integrity using @@ -220,6 +122,3 @@ Qualimap's output structure. - **RSeQC:** Wang L, Wang S, Li W. RSeQC: quality control of RNA-seq experiments. *Bioinformatics*. 2012;28(16):2184-2185. [RSeQC website](https://rseqc.sourceforge.net/) -- **Qualimap:** Garcia-Alcalde F, et al. Qualimap: evaluating next-generation - sequencing alignment data. *Bioinformatics*. 2012;28(20):2678-2679. - [Qualimap website](http://qualimap.conesalab.org/) diff --git a/docs/src/content/docs/usage/cli-reference.md b/docs/src/content/docs/usage/cli-reference.md index bff7bb4..ef8e9ad 100644 --- a/docs/src/content/docs/usage/cli-reference.md +++ b/docs/src/content/docs/usage/cli-reference.md @@ -139,8 +139,9 @@ printed and biotype counting is skipped. Write all output files directly into the output directory instead of organizing them into subdirectories. By default, RustQC creates `dupradar/`, -`featurecounts/`, and `rseqc//` subdirectories under the output directory. -With `--flat-output`, all files are written to the top-level output directory. +`featurecounts/`, `rseqc//`, `qualimap/`, `preseq/`, and `samtools/` +subdirectories under the output directory. With `--flat-output`, all files are +written to the top-level output directory. This can also be set in the [configuration file](/usage/configuration/) as `flat_output: true`. diff --git a/docs/src/content/docs/usage/configuration.md b/docs/src/content/docs/usage/configuration.md index 1473f48..7b2d9a7 100644 --- a/docs/src/content/docs/usage/configuration.md +++ b/docs/src/content/docs/usage/configuration.md @@ -301,15 +301,29 @@ tin: Requires annotation (`--gtf` or `--bed`). The TIN (Transcript Integrity Number) measures transcript integrity via Shannon entropy of read coverage uniformity. +### qualimap + +```yaml +qualimap: + enabled: true # Set to false to skip Qualimap RNA-Seq QC analysis +``` + +Requires annotation (`--gtf` only). Runs the Qualimap RNA-Seq QC analysis: +gene body coverage profiling (100 percentile bins, 5'→3'), 5'/3' bias metrics, +read origin classification (exonic/intronic/intergenic), strand-specificity +estimation, and splice junction motif counting. Produces Qualimap-compatible +output files parseable by MultiQC. + ### genebody_coverage ```yaml genebody_coverage: - enabled: true # Set to false to skip gene body coverage + enabled: true # Legacy toggle for the older gene body coverage module ``` -Requires annotation (`--gtf` only). Computes coverage profiles along transcript -bodies (100 percentile bins, 5'->3') and produces Qualimap-compatible output. +Requires annotation (`--gtf` only). This is a legacy config key for the +original gene body coverage implementation. The `qualimap:` section above +controls the current Qualimap-compatible gene body coverage analysis. ### preseq diff --git a/src/config.rs b/src/config.rs index cfd4807..15934fb 100644 --- a/src/config.rs +++ b/src/config.rs @@ -112,6 +112,10 @@ pub struct Config { /// preseq lc_extrap library complexity extrapolation configuration. #[serde(default)] pub preseq: PreseqConfig, + + /// Qualimap RNA-Seq QC configuration. + #[serde(default)] + pub qualimap: QualimapConfig, } // ============================================================================ @@ -529,6 +533,31 @@ impl Default for GenebodyCoverageConfig { } } +/// Configuration for Qualimap RNA-Seq QC. +/// +/// When enabled, produces Qualimap-compatible output files including +/// `rnaseq_qc_results.txt`, coverage profiles (total/high/low), plots, +/// and an HTML report. Uses Qualimap-compatible counting logic: +/// enclosure-based gene assignment with M-only CIGAR parsing. +/// +/// Example: +/// ```yaml +/// qualimap: +/// enabled: true +/// ``` +#[derive(Debug, Deserialize)] +#[serde(default)] +pub struct QualimapConfig { + /// Whether to produce Qualimap RNA-Seq QC output. Defaults to true. + pub enabled: bool, +} + +impl Default for QualimapConfig { + fn default() -> Self { + Self { enabled: true } + } +} + /// Configuration for samtools idxstats-compatible output. /// /// When enabled, produces a file matching `samtools idxstats` output format, diff --git a/src/main.rs b/src/main.rs index 1a543c7..766e487 100644 --- a/src/main.rs +++ b/src/main.rs @@ -412,6 +412,7 @@ fn run_rna(args: cli::RnaArgs) -> Result<()> { tin_index: tin_index.as_ref(), tin_sample_size: config.tin.sample_size.unwrap_or(100) as usize, tin_min_coverage: config.tin.min_coverage.unwrap_or(10), + gtf_path: args.gtf.as_deref(), }; // Step 2: Process all alignment files (in parallel when multiple) @@ -543,6 +544,8 @@ struct SharedParams<'a> { tin_sample_size: usize, /// Minimum read-start count per transcript to compute TIN. tin_min_coverage: u32, + /// Path to GTF file (for Qualimap report output). + gtf_path: Option<&'a str>, } // ============================================================================ @@ -650,6 +653,13 @@ fn process_single_bam( None }; + // === Build Qualimap exon index (if enabled, GTF-only) === + let qualimap_index = if params.config.qualimap.enabled { + genes.map(rna::qualimap::QualimapIndex::from_genes) + } else { + None + }; + // === dupRadar counting (requires GTF) === let mut count_result = if let Some(genes) = genes { info!( @@ -678,6 +688,7 @@ fn process_single_bam( None }, genebody_position_map.as_ref(), + qualimap_index.as_ref(), )?; info!( "[{}] Counting complete in {:.2}s", @@ -1023,41 +1034,26 @@ fn process_single_bam( stats.f_regions_duplication * 100.0 ); } - // === Gene body coverage output === - if let Some(ref gb_result) = count_result.genebody { - let gb_dir = if params.flat_output { + // === Qualimap RNA-Seq QC output === + if let (Some(ref qm_result), Some(ref qm_index)) = (&count_result.qualimap, &qualimap_index) + { + let qm_dir = if params.flat_output { outdir.to_path_buf() } else { outdir.join("qualimap") }; - std::fs::create_dir_all(&gb_dir)?; - let profile_path = gb_dir.join("coverage_profile_along_genes_(total).txt"); - rna::genebody::write_coverage_profile(gb_result, &profile_path)?; - info!( - "[{}] Gene body coverage profile written to {:?}", - bam_stem, profile_path - ); - - let qualimap_path = gb_dir.join("rnaseq_qc_results.txt"); - // Get total_records and secondary+supplementary from the bam_stat accumulator. - // bam_stat.total_records counts every BAM record (unfiltered), matching Qualimap's - // "total alignments". Fall back to dupRadar's stat_total_reads if bam_stat is disabled. - let (total_alignments, secondary) = rseqc_accums - .as_ref() - .and_then(|a| a.bam_stat.as_ref()) - .map(|bs| (bs.total_records, bs.secondary + bs.supplementary)) - .unwrap_or((count_result.stat_total_reads, 0)); - rna::genebody::write_qualimap_results( - gb_result, - bam_stem, - total_alignments, - secondary, - &qualimap_path, + rna::qualimap::output::write_qualimap_results( + qm_result, + qm_index, + bam_path, + params.gtf_path.unwrap_or(""), + params.stranded, + &qm_dir, )?; info!( - "[{}] Qualimap-compatible results written to {:?}", - bam_stem, qualimap_path + "[{}] Qualimap RNA-Seq QC results written to {:?}", + bam_stem, qm_dir ); } } // end if let Some(count_result) — GTF-only outputs diff --git a/src/rna/dupradar/counting.rs b/src/rna/dupradar/counting.rs index a3cd68f..2e12f21 100644 --- a/src/rna/dupradar/counting.rs +++ b/src/rna/dupradar/counting.rs @@ -11,6 +11,7 @@ use crate::gtf::Gene; use crate::rna::genebody::GenebodyCoverageAccum; +use crate::rna::qualimap::QualimapAccum; use crate::rna::rseqc::accumulators::{RseqcAccumulators, RseqcAnnotations, RseqcConfig}; use anyhow::{Context, Result}; use coitrees::{COITree, Interval, IntervalTree}; @@ -355,7 +356,11 @@ pub struct CountResult { /// Accumulated RSeQC tool results, if RSeQC tools were enabled pub rseqc: Option, /// Gene body coverage results (Qualimap-compatible). + #[allow(dead_code)] pub genebody: Option, + /// Qualimap RNA-Seq QC results (if enabled). + #[allow(dead_code)] + pub qualimap: Option, } /// Metadata stored with each interval in the cache-oblivious interval tree. @@ -582,6 +587,8 @@ struct ChromResult { fc_unmapped: u64, /// Gene body coverage accumulator (if enabled). genebody: Option, + /// Qualimap RNA-Seq QC accumulator (if enabled). + qualimap: Option, } impl ChromResult { @@ -608,6 +615,7 @@ impl ChromResult { fc_multimapping: 0, fc_unmapped: 0, genebody: None, + qualimap: None, } } @@ -647,6 +655,14 @@ impl ChromResult { self.genebody = Some(other_gb); } } + // Merge Qualimap accumulator + if let Some(other_qm) = other.qualimap { + if let Some(ref mut self_qm) = self.qualimap { + self_qm.merge(other_qm); + } else { + self.qualimap = Some(other_qm); + } + } } } @@ -697,11 +713,15 @@ fn process_chromosome_batch( rseqc_annotations: Option<&RseqcAnnotations>, htslib_threads: usize, genebody_position_map: Option<&crate::rna::genebody::TranscriptPositionMap>, + qualimap_index: Option<&crate::rna::qualimap::QualimapIndex>, ) -> Result<(ChromResult, Option)> { let mut result = ChromResult::new(num_genes); if genebody_position_map.is_some() { result.genebody = Some(crate::rna::genebody::GenebodyCoverageAccum::new()); } + if qualimap_index.is_some() { + result.qualimap = Some(crate::rna::qualimap::QualimapAccum::new(stranded)); + } let mut rseqc_accums = rseqc_config.map(|cfg| RseqcAccumulators::new(cfg, rseqc_annotations)); // Pre-compute resolved chromosome names for RSeQC tools. @@ -792,6 +812,17 @@ fn process_chromosome_batch( accums.process_read(&record, chrom, chrom_upper, annots, cfg); } + // --- Qualimap per-read dispatch (before counting filters) --- + // Qualimap accumulator handles its own filtering (unmapped, secondary, + // QC-fail, supplementary, NH>1) and uses enclosure-based gene assignment. + if let Some(ref mut qm) = result.qualimap { + let tid = record.tid(); + if tid >= 0 && (tid as usize) < tid_to_gtf_chrom.len() { + let qm_chrom = &tid_to_gtf_chrom[tid as usize]; + qm.process_read(&record, qm_chrom, qualimap_index.unwrap()); + } + } + let flags = record.flags(); // Skip unmapped reads (count for featureCounts summary) @@ -885,12 +916,12 @@ fn process_chromosome_batch( if gene_hits.is_empty() { result.stat_no_features += 1; if let Some(ref mut gb) = result.genebody { - gb.record_no_feature(&aligned_blocks_buf); + gb.record_no_feature(&aligned_blocks_buf, 1); } } else if gene_hits.len() > 1 { result.stat_ambiguous += 1; if let Some(ref mut gb) = result.genebody { - gb.record_ambiguous(); + gb.record_ambiguous(1); } } else if assign_fragment_to_gene( &gene_hits, @@ -902,7 +933,7 @@ fn process_chromosome_batch( if let (Some(ref mut gb), Some(pos_map)) = (&mut result.genebody, genebody_position_map) { - gb.record_coverage(gene_hits[0] as usize, &aligned_blocks_buf, pos_map); + gb.record_coverage(gene_hits[0] as usize, &aligned_blocks_buf, pos_map, 1); } } continue; @@ -948,36 +979,33 @@ fn process_chromosome_batch( result.n_unique_nodup += 1; } + // Qualimap uses intersection: a gene must appear in BOTH mates' strand-filtered + // gene hits to be considered. If either mate has no hits the fragment is + // no-feature. This matches HTSeq / Qualimap behaviour for paired-end mode. let combined_genes: Vec = - if mate_info.gene_hits.is_empty() && gene_hits.is_empty() { + if mate_info.gene_hits.is_empty() || gene_hits.is_empty() { Vec::new() } else { - let mut scores: HashMap = HashMap::new(); - for &g in &mate_info.gene_hits { - *scores.entry(g).or_insert(0) += 1; - } - for &g in &gene_hits { - *scores.entry(g).or_insert(0) += 1; - } - let max_score = scores.values().copied().max().unwrap_or(0); - let mut best: Vec = scores + // Intersect: keep only genes present in both mates + let mut intersection: Vec = mate_info + .gene_hits .iter() - .filter(|(_, &s)| s == max_score) - .map(|(&g, _)| g) + .filter(|g| gene_hits.contains(g)) + .copied() .collect(); - best.sort_unstable(); - best + intersection.sort_unstable(); + intersection }; if combined_genes.is_empty() { result.stat_no_features += 1; if let Some(ref mut gb) = result.genebody { - gb.record_no_feature(&aligned_blocks_buf); + gb.record_no_feature(&aligned_blocks_buf, 2); } } else if combined_genes.len() > 1 { result.stat_ambiguous += 1; if let Some(ref mut gb) = result.genebody { - gb.record_ambiguous(); + gb.record_ambiguous(2); } } else if assign_fragment_to_gene( &combined_genes, @@ -993,6 +1021,7 @@ fn process_chromosome_batch( combined_genes[0] as usize, &aligned_blocks_buf, pos_map, + 2, ); } } @@ -1055,6 +1084,7 @@ pub fn count_reads( rseqc_config: Option<&RseqcConfig>, rseqc_annotations: Option<&RseqcAnnotations>, genebody_position_map: Option<&crate::rna::genebody::TranscriptPositionMap>, + qualimap_index: Option<&crate::rna::qualimap::QualimapIndex>, ) -> Result { // Build gene ID interner for allocation-free lookups in the hot loop let interner = GeneIdInterner::from_genes(genes); @@ -1167,6 +1197,7 @@ pub fn count_reads( rseqc_annotations, htslib_threads, genebody_position_map, + qualimap_index, ) }) .collect() @@ -1197,6 +1228,8 @@ pub fn count_reads( } let mut rseqc_accums: Option = rseqc_config.map(|cfg| RseqcAccumulators::new(cfg, rseqc_annotations)); + let mut qualimap_accum: Option = + qualimap_index.map(|_| crate::rna::qualimap::QualimapAccum::new(stranded)); // Pre-compute resolved chromosome names for RSeQC tools // (apply chromosome prefix and mapping, same as parallel path) @@ -1264,6 +1297,17 @@ pub fn count_reads( accums.process_read(&record, chrom, chrom_upper, annots, cfg); } + // --- Qualimap per-read dispatch (before counting filters) --- + // Qualimap has its own filtering (M-only CIGAR, NH>1, enclosure-based) + if let (Some(ref mut qm_accum), Some(qm_index)) = (&mut qualimap_accum, qualimap_index) + { + let tid = record.tid(); + if tid >= 0 && (tid as usize) < tid_to_rseqc_chrom.len() { + let chrom = &tid_to_rseqc_chrom[tid as usize]; + qm_accum.process_read(&record, chrom, qm_index); + } + } + if flags & BAM_FUNMAP != 0 { result.fc_unmapped += 1; continue; @@ -1341,12 +1385,12 @@ pub fn count_reads( if gene_hits.is_empty() { result.stat_no_features += 1; if let Some(ref mut gb) = result.genebody { - gb.record_no_feature(&aligned_blocks_buf); + gb.record_no_feature(&aligned_blocks_buf, 1); } } else if gene_hits.len() > 1 { result.stat_ambiguous += 1; if let Some(ref mut gb) = result.genebody { - gb.record_ambiguous(); + gb.record_ambiguous(1); } } else if assign_fragment_to_gene( &gene_hits, @@ -1358,7 +1402,7 @@ pub fn count_reads( if let (Some(ref mut gb), Some(pos_map)) = (&mut result.genebody, genebody_position_map) { - gb.record_coverage(gene_hits[0] as usize, &aligned_blocks_buf, pos_map); + gb.record_coverage(gene_hits[0] as usize, &aligned_blocks_buf, pos_map, 1); } } continue; @@ -1417,18 +1461,30 @@ pub fn count_reads( result.n_unique_nodup += 1; } + // Intersection: gene must appear in BOTH mates (Qualimap behaviour) let combined_genes: Vec = - merge_gene_hits(&mate_info.gene_hits, &gene_hits); + if mate_info.gene_hits.is_empty() || gene_hits.is_empty() { + Vec::new() + } else { + let mut intersection: Vec = mate_info + .gene_hits + .iter() + .filter(|g| gene_hits.contains(g)) + .copied() + .collect(); + intersection.sort_unstable(); + intersection + }; if combined_genes.is_empty() { result.stat_no_features += 1; if let Some(ref mut gb) = result.genebody { - gb.record_no_feature(&aligned_blocks_buf); + gb.record_no_feature(&aligned_blocks_buf, 2); } } else if combined_genes.len() > 1 { result.stat_ambiguous += 1; if let Some(ref mut gb) = result.genebody { - gb.record_ambiguous(); + gb.record_ambiguous(2); } } else if assign_fragment_to_gene( &combined_genes, @@ -1444,6 +1500,7 @@ pub fn count_reads( combined_genes[0] as usize, &aligned_blocks_buf, pos_map, + 2, ); } } @@ -1461,6 +1518,7 @@ pub fn count_reads( } result.unmatched_mates = mate_buffer; + result.qualimap = qualimap_accum; (result, rseqc_accums) }; @@ -1642,6 +1700,13 @@ pub fn count_reads( genebody: merged .genebody .map(|a: GenebodyCoverageAccum| a.into_result()), + qualimap: match (merged.qualimap, qualimap_index) { + (Some(mut a), Some(idx)) => { + a.flush_unpaired(idx); + Some(a.into_result(idx)) + } + _ => None, + }, }) } diff --git a/src/rna/featurecounts/output.rs b/src/rna/featurecounts/output.rs index db4f98d..eda1ec3 100644 --- a/src/rna/featurecounts/output.rs +++ b/src/rna/featurecounts/output.rs @@ -331,6 +331,7 @@ mod tests { fc_unmapped: 0, rseqc: None, genebody: None, + qualimap: None, }; let biotypes = aggregate_biotype_counts(&genes, &count_result, "gene_biotype"); diff --git a/src/rna/genebody.rs b/src/rna/genebody.rs index b247314..67a3fbd 100644 --- a/src/rna/genebody.rs +++ b/src/rna/genebody.rs @@ -164,18 +164,21 @@ impl GenebodyCoverageAccum { /// * `gene_idx` - Index of the assigned gene /// * `aligned_blocks` - Read's aligned genomic blocks (0-based half-open) /// * `position_map` - Precomputed exon position map + /// * `read_count` - Number of reads in this fragment (1 for single-end, 2 for paired-end). + /// Qualimap counts reads, not fragments, so aligned_to_genes increments by read_count. pub fn record_coverage( &mut self, gene_idx: usize, aligned_blocks: &[(u64, u64)], position_map: &TranscriptPositionMap, + read_count: u64, ) { let gene_map = match position_map.get(gene_idx) { Some(m) => m, None => return, }; - self.aligned_to_genes += 1; + self.aligned_to_genes += read_count; // Track exon overlap count for overlapping_exon metric let mut exons_hit = 0u32; @@ -257,16 +260,20 @@ impl GenebodyCoverageAccum { } /// Record a read that was not assigned to any gene (intergenic). - pub fn record_no_feature(&mut self, aligned_blocks: &[(u64, u64)]) { - self.no_feature += 1; + /// + /// `read_count` is 1 for single-end, 2 for paired-end (Qualimap counts reads not fragments). + pub fn record_no_feature(&mut self, aligned_blocks: &[(u64, u64)], read_count: u64) { + self.no_feature += read_count; for &(start, end) in aligned_blocks { self.intergenic += end - start; } } /// Record an ambiguous read (overlapping multiple genes). - pub fn record_ambiguous(&mut self) { - self.ambiguous += 1; + /// + /// `read_count` is 1 for single-end, 2 for paired-end (Qualimap counts reads not fragments). + pub fn record_ambiguous(&mut self, read_count: u64) { + self.ambiguous += read_count; } /// Merge another accumulator into this one. @@ -289,6 +296,7 @@ impl GenebodyCoverageAccum { // ============================================================ /// Gene body coverage results. +#[allow(dead_code)] #[derive(Debug)] pub struct GenebodyCoverageResult { /// Coverage profile bins (100 percentile bins). @@ -364,6 +372,7 @@ impl GenebodyCoverageAccum { /// Write the coverage profile along genes in Qualimap format. /// /// Format: TSV with columns `position` (0.0–99.0) and `coverage` (cumulative depth). +#[allow(dead_code)] pub fn write_coverage_profile(result: &GenebodyCoverageResult, output_path: &Path) -> Result<()> { let mut f = std::fs::File::create(output_path) .with_context(|| format!("Failed to create {}", output_path.display()))?; @@ -377,6 +386,7 @@ pub fn write_coverage_profile(result: &GenebodyCoverageResult, output_path: &Pat } /// Format a number with comma-separated thousands. +#[allow(dead_code)] fn format_with_commas(n: u64) -> String { let s = n.to_string(); let mut result = String::with_capacity(s.len() + s.len() / 3); @@ -392,6 +402,7 @@ fn format_with_commas(n: u64) -> String { /// Write Qualimap rnaseq-compatible results file. /// /// Format matches `rnaseq_qc_results.txt` expected by MultiQC. +#[allow(dead_code)] pub fn write_qualimap_results( result: &GenebodyCoverageResult, bam_path: &str, diff --git a/src/rna/mod.rs b/src/rna/mod.rs index a3925b7..60dbe0c 100644 --- a/src/rna/mod.rs +++ b/src/rna/mod.rs @@ -7,4 +7,5 @@ pub mod dupradar; pub mod featurecounts; pub mod genebody; pub mod preseq; +pub mod qualimap; pub mod rseqc; diff --git a/src/rna/preseq.rs b/src/rna/preseq.rs index 8392b71..fda26c4 100644 --- a/src/rna/preseq.rs +++ b/src/rna/preseq.rs @@ -1371,7 +1371,7 @@ mod tests { #[test] fn test_bootstrap_reproducibility() { let hist = vec![(1, 100), (2, 50), (3, 25)]; - let total_reads = 225; + let _total_reads = 225; let mut rng1 = ChaCha8Rng::seed_from_u64(42); let (h1, t1, d1) = bootstrap_resample(&hist, &mut rng1); diff --git a/src/rna/qualimap/accumulator.rs b/src/rna/qualimap/accumulator.rs new file mode 100644 index 0000000..2fa3d9f --- /dev/null +++ b/src/rna/qualimap/accumulator.rs @@ -0,0 +1,1127 @@ +//! Qualimap-compatible RNA-Seq QC accumulator. +//! +//! Processes BAM records using Qualimap's counting rules: +//! - M-only CIGAR blocks (no insertion/deletion/softclip contribution) +//! - Enclosure-based gene assignment (each M-block must be fully contained in exons of the same gene) +//! - PE reads: combine both mates' M-blocks, assign on combined set, count numReads=2 +//! - Multi-mappers excluded entirely (NH > 1) +//! - Junction motif extraction from read sequence at N-operation boundaries + +use std::collections::{HashMap, HashSet}; + +use coitrees::IntervalTree; +use rust_htslib::bam; +use rust_htslib::bam::record::Cigar; + +use super::coverage::{MergedGeneCoverage, TranscriptCoverage}; +use super::index::QualimapIndex; + +// ============================================================ +// Cached tree query result for a single M-block +// ============================================================ + +/// Pre-computed results from a single merged exon tree query for one M-block. +/// +/// By querying the tree once per block and caching the results, we avoid +/// redundant COITree queries across `find_enclosing_genes`, +/// `add_per_block_coverage`, `check_overlapping_exon`, and +/// `count_ssp_for_blocks`. +#[derive(Debug, Clone)] +struct CachedBlockHits { + /// Genes whose merged exon fully encloses this M-block, with their strand. + /// Deduplicated by `gene_idx`; each gene appears at most once. + enclosing_genes: Vec<(u32, u8)>, + /// Whether any node overlaps this M-block without fully enclosing it. + /// Used for the Qualimap `overlapping_exon` counter. + has_overlap_not_enclosed: bool, +} + +// ============================================================ +// BAM flag constants +// ============================================================ + +const BAM_FUNMAP: u16 = 0x4; +const BAM_FSECONDARY: u16 = 0x100; +const BAM_FQCFAIL: u16 = 0x200; +const BAM_FSUPPLEMENTARY: u16 = 0x800; +const BAM_FPAIRED: u16 = 0x1; +const BAM_FPROPER_PAIR: u16 = 0x2; +const BAM_FREAD1: u16 = 0x40; +const BAM_FREAD2: u16 = 0x80; +const BAM_FREVERSE: u16 = 0x10; + +// ============================================================ +// Mate buffer for PE reads +// ============================================================ + +/// Key for mate buffering: (qname_hash, r1_tid, r1_pos, r2_tid, r2_pos). +type MateKey = (u64, i32, i64, i32, i64); + +/// A splice junction motif extracted from the read sequence at an N-operation. +#[derive(Debug, Clone)] +struct JunctionMotif { + /// 2bp donor motif (from read, e.g., "GT"). + donor: [u8; 2], + /// 2bp acceptor motif (from read, e.g., "AG"). + acceptor: [u8; 2], +} + +/// Per-mate data passed through the PE reconciliation pipeline. +/// +/// Groups the per-read data needed for `reconcile_pair()` and +/// `classify_and_count()`, reducing parameter counts. +#[derive(Debug, Clone)] +struct MateData { + /// M-only aligned blocks (0-based half-open). + m_blocks: Vec<(i32, i32)>, + /// Genes whose exons enclose ALL M-blocks of this mate. + enclosing_genes: HashSet, + /// Splice junction motifs extracted from N-operations. + junction_motifs: Vec, + /// Cached per-block tree query results for this mate. + cached_hits: Vec, + /// Whether this mate is on the reverse strand (flag 0x10). + is_reverse: bool, + /// Whether this mate is the first read in pair (flag 0x40). + is_first_of_pair: bool, +} + +// ============================================================ +// Qualimap counters +// ============================================================ + +/// Accumulated Qualimap-compatible QC counters. +/// +/// These match the counters in Qualimap's `RNASeqQCAnalysis` and are output +/// in `rnaseq_qc_results.txt`. +#[derive(Debug, Clone, Default)] +pub struct QualimapCounters { + /// Total primary alignments processed. + pub primary_alignments: u64, + /// Total secondary alignments seen (skipped). + pub secondary_alignments: u64, + /// Unmapped reads (flag 0x4). + pub not_aligned: u64, + /// Multi-mapped reads (NH > 1), excluded from counting. + pub alignment_not_unique: u64, + /// Reads assigned to exactly one gene (exonic). + pub exonic_reads: u64, + /// Reads not assigned to any gene and not intronic (intergenic). + pub no_feature: u64, + /// Reads assigned to more than one gene. + pub ambiguous: u64, + /// Reads with any M-block overlapping an intron. + pub intronic_reads: u64, + /// Reads not overlapping any exon or intron. + pub intergenic_reads: u64, + /// No-feature reads that overlap an exon region ("intronic/intergenic + /// overlapping exon" in Qualimap terminology). Only counted once per + /// read/fragment that has any M-block overlapping an exon. + pub overlapping_exon: u64, + /// Total reads counted (numReads: for PE, 2 per fragment). + pub read_count: u64, + /// Total fragments counted (PE: 1 per pair, SE: 1 per read). + pub fragment_count: u64, + /// Left mates in proper pairs (flag 0x2 + 0x40). + pub left_proper_in_pair: u64, + /// Right mates in proper pairs (flag 0x2 + 0x80). + pub right_proper_in_pair: u64, + /// Both mates with proper-pair flag set (for numberOfMappedPairs = count / 2). + pub both_proper_in_pair: u64, + /// Reads at splice junctions (with N-operations in CIGAR). + pub reads_at_junctions: u64, + /// Total supplementary alignments seen (skipped). + pub supplementary: u64, + /// SSP forward-strand estimation counter. + pub ssp_fwd: u64, + /// SSP reverse-strand estimation counter. + pub ssp_rev: u64, +} + +impl QualimapCounters { + /// Merge counters from another accumulator. + pub fn merge(&mut self, other: &QualimapCounters) { + self.primary_alignments += other.primary_alignments; + self.secondary_alignments += other.secondary_alignments; + self.not_aligned += other.not_aligned; + self.alignment_not_unique += other.alignment_not_unique; + self.exonic_reads += other.exonic_reads; + self.no_feature += other.no_feature; + self.ambiguous += other.ambiguous; + self.intronic_reads += other.intronic_reads; + self.intergenic_reads += other.intergenic_reads; + self.overlapping_exon += other.overlapping_exon; + self.read_count += other.read_count; + self.fragment_count += other.fragment_count; + self.left_proper_in_pair += other.left_proper_in_pair; + self.right_proper_in_pair += other.right_proper_in_pair; + self.both_proper_in_pair += other.both_proper_in_pair; + self.reads_at_junctions += other.reads_at_junctions; + self.supplementary += other.supplementary; + self.ssp_fwd += other.ssp_fwd; + self.ssp_rev += other.ssp_rev; + } +} + +// ============================================================ +// Junction motif accumulator +// ============================================================ + +/// Accumulated junction motif counts (donor-acceptor pairs). +#[derive(Debug, Clone, Default)] +pub struct JunctionMotifCounts { + /// Counts keyed by (donor_2bp, acceptor_2bp) as uppercase ASCII. + pub counts: HashMap<([u8; 2], [u8; 2]), u64>, +} + +impl JunctionMotifCounts { + /// Merge counts from another accumulator. + pub fn merge(&mut self, other: &JunctionMotifCounts) { + for (key, &count) in &other.counts { + *self.counts.entry(*key).or_insert(0) += count; + } + } +} + +// ============================================================ +// QualimapAccum — the main accumulator +// ============================================================ + +/// Qualimap RNA-Seq QC accumulator. +/// +/// Processes BAM records using Qualimap's counting rules and accumulates: +/// - Read/fragment classification counters +/// - Per-transcript coverage +/// - Junction motif counts +/// +/// This accumulator is designed to integrate into the existing BAM pass via +/// `RseqcAccumulators`, receiving each BAM record through `process_read()`. +#[derive(Debug, Clone)] +pub struct QualimapAccum { + /// QC counters matching Qualimap's output. + pub counters: QualimapCounters, + /// Per-transcript per-base coverage. + pub coverage: TranscriptCoverage, + /// Per-gene merged-model coverage. + pub merged_gene_coverage: MergedGeneCoverage, + /// Junction splice motif counts. + pub junction_motifs: JunctionMotifCounts, + /// Mate buffer for PE reconciliation. + mate_buffer: HashMap, + /// Strandedness protocol: 0=unstranded, 1=forward, 2=reverse. + stranded: u8, +} + +impl QualimapAccum { + /// Create a new Qualimap accumulator. + /// + /// # Arguments + /// * `stranded` - Strandedness: 0=unstranded, 1=forward, 2=reverse. + pub fn new(stranded: u8) -> Self { + Self { + counters: QualimapCounters::default(), + coverage: TranscriptCoverage::new(), + merged_gene_coverage: MergedGeneCoverage::new(), + junction_motifs: JunctionMotifCounts::default(), + mate_buffer: HashMap::new(), + stranded, + } + } + + /// Process a single BAM record. + /// + /// Applies Qualimap's filtering and counting logic: + /// 1. Skip unmapped, secondary, QC-fail, supplementary reads + /// 2. Skip multi-mappers (NH > 1) + /// 3. Extract M-only CIGAR blocks + /// 4. For SE: assign immediately via enclosure check + /// 5. For PE: buffer mate, assign when pair is complete + /// + /// # Arguments + /// * `record` - The BAM record to process. + /// * `chrom` - Chromosome name for this record. + /// * `index` - The Qualimap annotation index. + pub fn process_read(&mut self, record: &bam::Record, chrom: &str, index: &QualimapIndex) { + let flags = record.flags(); + log::trace!( + "QM process_read chrom={} flags={} pos={}", + chrom, + flags, + record.pos() + ); + + // Skip unmapped + if flags & BAM_FUNMAP != 0 { + self.counters.not_aligned += 1; + return; + } + + // Multi-mapper check on ALL mapped reads (including secondary). + // Qualimap increments alignmentNotUnique before the skipSecondary check, + // so secondary reads with NH>1 are counted in both secondary AND non-unique. + let is_multi_mapped = get_nh_tag(record).is_some_and(|nh| nh > 1); + if is_multi_mapped { + self.counters.alignment_not_unique += 1; + } + + // Track secondary vs primary + let is_secondary = flags & BAM_FSECONDARY != 0; + if is_secondary { + self.counters.secondary_alignments += 1; + // Qualimap skipSecondary=true by default in RNA-Seq mode. + // Secondary reads are counted but excluded from all downstream + // gene assignment, SSP, and junction analysis. + return; + } + self.counters.primary_alignments += 1; + + // Count left/right reads for ALL primary paired reads (not just proper pair). + // Qualimap: leftProperInPair counts first-of-pair, rightProperInPair counts + // second-of-pair — despite the name, they don't check the proper-pair flag. + // bothProperInPair counts reads that ARE proper pair (used for numberOfMappedPairs). + if flags & BAM_FPAIRED != 0 { + if flags & BAM_FREAD1 != 0 { + self.counters.left_proper_in_pair += 1; + } + if flags & BAM_FREAD2 != 0 { + self.counters.right_proper_in_pair += 1; + } + if flags & BAM_FPROPER_PAIR != 0 { + self.counters.both_proper_in_pair += 1; + } + } + + // Skip supplementary and QC-fail (these never contribute) + if flags & BAM_FSUPPLEMENTARY != 0 { + self.counters.supplementary += 1; + return; + } + if flags & BAM_FQCFAIL != 0 { + return; + } + + // readCount: primary reads that pass initial filters + // (Qualimap: readCount counts all non-secondary, non-supplementary reads) + self.counters.read_count += 1; + + // Extract M-only CIGAR blocks (replicating Qualimap's CIGAR bug where + // offset += length for ALL operations, including I/S/H/P). + let m_blocks = extract_m_blocks(record); + + // Skip multi-mappers from gene assignment, junction counting, and coverage. + // Coverage is added only for uniquely-mapped reads, restricted to fully-enclosed + // M-blocks, matching the correct Qualimap coverage model. + if is_multi_mapped { + return; + } + if m_blocks.is_empty() { + return; + } + + // Extract junction motifs from N-operations in CIGAR. + // Only uniquely-mapped primary reads contribute junctions. + let (n_op_count, motifs) = extract_junction_motifs(record); + // Qualimap increments numReadsWithJunction for every N-operation, + // even when the motif extraction guard fails. Match that behavior. + self.counters.reads_at_junctions += n_op_count as u64; + + // --- Cache tree query results for all M-blocks --- + // Query the merged exon tree ONCE per block set and reuse the results + // across enclosure check, coverage, overlapping-exon, and SSP. + let cached_hits = cache_block_hits(&m_blocks, chrom, index); + + // Determine enclosing genes using cached results (with strand filtering) + let is_reverse = flags & BAM_FREVERSE != 0; + let is_first_of_pair = flags & BAM_FREAD1 != 0; + let enclosing_genes = + find_enclosing_genes_cached(&cached_hits, self.stranded, is_reverse, is_first_of_pair); + + // --- Coverage: per-block, strand-independent (Qualimap model) --- + // Qualimap adds coverage per M-block to each enclosing gene, without + // strand filtering. This is separate from gene assignment counting. + // For SE reads: add coverage now. For PE: deferred to reconcile_pair(). + if flags & BAM_FPAIRED == 0 || flags & BAM_FPROPER_PAIR == 0 { + self.add_per_block_coverage_cached(&m_blocks, &cached_hits, index); + } + + // Bundle per-read data for downstream use + let data = MateData { + m_blocks, + enclosing_genes, + junction_motifs: motifs, + cached_hits, + is_reverse, + is_first_of_pair, + }; + + // PE path: check BAM flags directly (no library-level paired flag needed) + if flags & BAM_FPAIRED != 0 && flags & BAM_FPROPER_PAIR != 0 { + // PE proper pair: buffer and combine with mate (Qualimap name-sorts + // and processes both mates' intervals together as a fragment). + self.process_pe_read(record, data, chrom, index); + } else { + // SE mode or non-proper pair: assign immediately (numReads = 1) + self.classify_and_count(&data, chrom, index, 1); + } + } + + /// Process a PE read — buffer first mate, reconcile when second arrives. + fn process_pe_read( + &mut self, + record: &bam::Record, + data: MateData, + chrom: &str, + index: &QualimapIndex, + ) { + let key = make_mate_key(record); + + if let Some(mate) = self.mate_buffer.remove(&key) { + // Found the mate — reconcile the pair. + // Current read is r1 (second-seen), buffered mate is r2 (first-seen). + self.reconcile_pair(&data, &mate, chrom, index); + } else { + // First mate seen — buffer it + self.mate_buffer.insert(key, data); + } + } + + /// Reconcile a PE pair: combine M-blocks and gene assignments. + /// + /// Qualimap intersects the enclosing gene sets of both mates. + /// If exactly one gene encloses ALL M-blocks of BOTH mates → assigned. + /// If >1 gene → ambiguous. If 0 genes → check intronic/intergenic. + fn reconcile_pair(&mut self, r1: &MateData, r2: &MateData, chrom: &str, index: &QualimapIndex) { + // Intersect the enclosing gene sets from both mates (already computed). + let assigned_genes: HashSet = r1 + .enclosing_genes + .intersection(&r2.enclosing_genes) + .copied() + .collect(); + + // --- Coverage: per-block, strand-independent (Qualimap model) --- + // Use cached hits from both mates to add coverage without re-querying the tree. + self.add_per_block_coverage_cached(&r1.m_blocks, &r1.cached_hits, index); + self.add_per_block_coverage_cached(&r2.m_blocks, &r2.cached_hits, index); + + // Collect junction motifs from both mates + for motif in r1.junction_motifs.iter().chain(r2.junction_motifs.iter()) { + *self + .junction_motifs + .counts + .entry((motif.donor, motif.acceptor)) + .or_insert(0) += 1; + } + + // Fragment assignment + self.counters.fragment_count += 1; + + // Check for overlapping_exon using cached hits from both mates. + // At most one increment per fragment: check r2 only if r1 didn't trigger. + if !check_has_overlap_not_enclosed(&r1.cached_hits) { + self.check_overlapping_exon_cached(&r2.cached_hits); + } else { + self.counters.overlapping_exon += 1; + } + + // Combine blocks for intronic/intergenic classification only when needed + match assigned_genes.len() { + 0 => { + // No gene encloses all blocks — classify as intronic or intergenic + let mut combined_blocks: Vec<(i32, i32)> = + Vec::with_capacity(r1.m_blocks.len() + r2.m_blocks.len()); + combined_blocks.extend_from_slice(&r1.m_blocks); + combined_blocks.extend_from_slice(&r2.m_blocks); + self.classify_no_feature(&combined_blocks, chrom, index, 2); + // Qualimap: noFeature += numReads (2 for PE fragment) + self.counters.no_feature += 2; + } + 1 => { + // Exactly one gene — assigned (exonic) + // Qualimap: exonicReads += numReads (2 for PE fragment) + self.counters.exonic_reads += 2; + } + _ => { + // Multiple genes — ambiguous + // Qualimap: ambiguous += numReads (2 for PE fragment) + self.counters.ambiguous += 2; + } + } + + // SSP estimation using cached hits — avoids re-querying the tree. + self.count_ssp_for_blocks_cached(&r1.cached_hits, r1.is_reverse, r1.is_first_of_pair); + let r2_is_first = !r1.is_first_of_pair; + self.count_ssp_for_blocks_cached(&r2.cached_hits, r2.is_reverse, r2_is_first); + } + + /// Classify and count a fragment (SE read or single-mate data). + /// + /// Shared logic for SE reads, non-proper pairs, and cross-chromosome + /// mate reconciliation. `num_reads` is 1 for SE / non-proper and 2 for + /// cross-chromosome PE fragments. + fn classify_and_count( + &mut self, + data: &MateData, + chrom: &str, + index: &QualimapIndex, + num_reads: u64, + ) { + // Record junction motifs + for motif in &data.junction_motifs { + *self + .junction_motifs + .counts + .entry((motif.donor, motif.acceptor)) + .or_insert(0) += 1; + } + + self.counters.fragment_count += 1; + + // Check for overlapping_exon using cached results. + self.check_overlapping_exon_cached(&data.cached_hits); + + match data.enclosing_genes.len() { + 0 => { + self.classify_no_feature(&data.m_blocks, chrom, index, num_reads); + self.counters.no_feature += num_reads; + } + 1 => { + self.counters.exonic_reads += num_reads; + } + _ => { + self.counters.ambiguous += num_reads; + } + } + + // SSP estimation using cached hits. + self.count_ssp_for_blocks_cached(&data.cached_hits, data.is_reverse, data.is_first_of_pair); + } + + /// Check if any M-block overlaps an exon region without being fully enclosed, + /// using pre-computed cached block hits. Increments the counter at most once. + fn check_overlapping_exon_cached(&mut self, cached_hits: &[CachedBlockHits]) { + if check_has_overlap_not_enclosed(cached_hits) { + self.counters.overlapping_exon += 1; + } + } + + /// Add per-transcript and merged-gene coverage, per-block, strand-independent. + /// + /// Uses pre-computed cached block hits to avoid redundant tree queries. + /// Matches Qualimap's coverage model exactly: coverage is added per-block + /// for every gene whose merged exon encloses that individual M-block. + /// + /// # Arguments + /// * `m_blocks` - M-only aligned blocks (0-based half-open). + /// * `cached_hits` - Pre-computed tree query results per block. + /// * `index` - Qualimap annotation index. + fn add_per_block_coverage_cached( + &mut self, + m_blocks: &[(i32, i32)], + cached_hits: &[CachedBlockHits], + index: &QualimapIndex, + ) { + for (i, &(block_start, block_end)) in m_blocks.iter().enumerate() { + let hit = &cached_hits[i]; + let single_block = &[(block_start, block_end)]; + for &(gidx, _strand) in &hit.enclosing_genes { + let (tx_start, _) = index.gene_transcript_ranges[gidx as usize]; + let transcripts = index.gene_transcripts(gidx); + self.coverage + .add_coverage(single_block, transcripts, tx_start); + if let Some(model) = index.merged_gene_models.get(gidx as usize) { + self.merged_gene_coverage + .add_coverage(gidx, single_block, model); + } + } + } + } + + /// Classify a read that wasn't assigned to any gene as intronic or intergenic. + fn classify_no_feature( + &mut self, + m_blocks: &[(i32, i32)], + chrom: &str, + index: &QualimapIndex, + num_reads: u64, + ) { + // Classify as intronic or intergenic + if let Some(intron_tree) = index.intron_tree(chrom) { + for &(start, end) in m_blocks { + let mut found_intron = false; + intron_tree.query(start, end, |_iv| { + found_intron = true; + }); + if found_intron { + self.counters.intronic_reads += num_reads; + return; + } + } + } + self.counters.intergenic_reads += num_reads; + } + + /// Count SSP votes using pre-computed cached block hits. + /// + /// Uses the `(gene_idx, strand)` pairs from cached hits directly — each gene + /// appears at most once per block (deduplicated in `cache_block_hits`), so no + /// additional deduplication is needed. + fn count_ssp_for_blocks_cached( + &mut self, + cached_hits: &[CachedBlockHits], + is_reverse: bool, + is_first_of_pair: bool, + ) { + for hit in cached_hits { + for &(_gidx, strand) in &hit.enclosing_genes { + let same_strand = (is_reverse && strand == b'-') || (!is_reverse && strand == b'+'); + if is_first_of_pair { + if same_strand { + self.counters.ssp_fwd += 1; + } else { + self.counters.ssp_rev += 1; + } + } else if same_strand { + self.counters.ssp_rev += 1; + } else { + self.counters.ssp_fwd += 1; + } + } + } + } + + /// Flush any remaining unpaired mates at the end of a chromosome batch. + /// + /// PE mates that were never reconciled are treated as singletons and + /// Qualimap skips proper-pair fragments where only one mate survived + /// filters (numSingleReadOnly). We simply discard orphaned mates. + #[allow(dead_code)] + pub fn flush_unpaired(&mut self, _index: &QualimapIndex) { + // Qualimap behaviour: if a proper-pair read's mate was filtered out + // (by NH>1, unmapped, etc.), the fragment is skipped entirely — + // neither exonic nor noFeature is counted. We match this by simply + // draining the mate buffer without processing. + self.mate_buffer.clear(); + } + + /// Merge another `QualimapAccum` into this one. + /// + /// Used when combining results from parallel chromosome batches. + pub fn merge(&mut self, other: QualimapAccum) { + self.counters.merge(&other.counters); + self.coverage.merge(other.coverage); + self.merged_gene_coverage.merge(other.merged_gene_coverage); + self.junction_motifs.merge(&other.junction_motifs); + + // Merge mate buffers (cross-chromosome mates). + // When both mates were buffered in different per-chromosome batches, + // reconcile them here. These are PE fragments, so num_reads = 2. + for (key, info) in other.mate_buffer { + if let Some(existing) = self.mate_buffer.remove(&key) { + // We don't have the chrom handy for intronic classification, + // so treat no-feature conservatively as intergenic. + self.counters.fragment_count += 1; + + let common_genes: HashSet = existing + .enclosing_genes + .intersection(&info.enclosing_genes) + .copied() + .collect(); + + // Union fallback: if one mate has no enclosing genes, use + // the other mate's set (cross-chrom pairs often have one + // mate in an unannotated region). + let assigned = if existing.enclosing_genes.is_empty() + && !info.enclosing_genes.is_empty() + { + info.enclosing_genes.clone() + } else if info.enclosing_genes.is_empty() && !existing.enclosing_genes.is_empty() { + existing.enclosing_genes.clone() + } else { + common_genes + }; + + // PE fragment: count both reads (num_reads = 2) + match assigned.len() { + 0 => { + self.counters.no_feature += 2; + self.counters.intergenic_reads += 2; + } + 1 => { + self.counters.exonic_reads += 2; + } + _ => { + self.counters.ambiguous += 2; + } + } + + // Junction motifs from both mates + for motif in existing + .junction_motifs + .iter() + .chain(info.junction_motifs.iter()) + { + *self + .junction_motifs + .counts + .entry((motif.donor, motif.acceptor)) + .or_insert(0) += 1; + } + } else { + self.mate_buffer.insert(key, info); + } + } + } + + /// Get the number of unmatched mates still in the buffer. + #[allow(dead_code)] + pub fn unmatched_count(&self) -> usize { + self.mate_buffer.len() + } + + /// Convert this accumulator into a `QualimapResult`. + /// + /// This should be called after all reads have been processed and + /// `flush_unpaired()` has been called. + pub fn into_result(self, index: &QualimapIndex) -> super::QualimapResult { + // Convert junction motif byte arrays to readable strings + let mut junction_motifs_str = HashMap::new(); + for ((donor, acceptor), count) in &self.junction_motifs.counts { + let motif = format!( + "{}{}{}{}", + donor[0] as char, donor[1] as char, acceptor[0] as char, acceptor[1] as char, + ); + *junction_motifs_str.entry(motif).or_insert(0u64) += count; + } + + // Build string-keyed coverage map from the raw coverage data, then + // take ownership of the raw coverage without cloning. + let mut transcript_coverage = HashMap::new(); + for (flat_idx, depth) in self.coverage.iter() { + if let Some(tx_info) = index.transcripts.get(flat_idx as usize) { + transcript_coverage.insert(tx_info.transcript_id.clone(), depth.to_vec()); + } + } + let transcript_coverage_raw = self.coverage; + + super::QualimapResult { + primary_alignments: self.counters.primary_alignments, + secondary_alignments: self.counters.secondary_alignments, + not_aligned: self.counters.not_aligned, + alignment_not_unique: self.counters.alignment_not_unique, + exonic_reads: self.counters.exonic_reads, + ambiguous_reads: self.counters.ambiguous, + no_feature: self.counters.no_feature, + intronic_reads: self.counters.intronic_reads, + intergenic_reads: self.counters.intergenic_reads, + overlapping_exon_reads: self.counters.overlapping_exon, + read_count: self.counters.read_count, + fragment_count: self.counters.fragment_count, + left_proper_in_pair: self.counters.left_proper_in_pair, + right_proper_in_pair: self.counters.right_proper_in_pair, + both_proper_in_pair: self.counters.both_proper_in_pair, + reads_at_junctions: self.counters.reads_at_junctions, + junction_motifs: junction_motifs_str, + transcript_coverage, + transcript_coverage_raw, + merged_gene_coverage: self.merged_gene_coverage, + ssp_fwd: self.counters.ssp_fwd, + ssp_rev: self.counters.ssp_rev, + } + } +} + +// ============================================================ +// Helper functions +// ============================================================ + +/// Extract NH tag (number of reported alignments) from a BAM record. +fn get_nh_tag(record: &bam::Record) -> Option { + match record.aux(b"NH") { + Ok(rust_htslib::bam::record::Aux::U8(v)) => Some(v as u32), + Ok(rust_htslib::bam::record::Aux::U16(v)) => Some(v as u32), + Ok(rust_htslib::bam::record::Aux::U32(v)) => Some(v), + Ok(rust_htslib::bam::record::Aux::I8(v)) => Some(v as u32), + Ok(rust_htslib::bam::record::Aux::I16(v)) => Some(v as u32), + Ok(rust_htslib::bam::record::Aux::I32(v)) => Some(v as u32), + _ => None, + } +} + +/// Extract M-only aligned blocks from a BAM record's CIGAR. +/// +/// Returns a vector of (start, end) in 0-based half-open coordinates. +/// Only `M` (alignment match) operations are included. +/// +/// Extract correct alignment blocks from a BAM record's CIGAR string. +/// +/// Unlike [`extract_m_blocks`], this function uses **correct** CIGAR semantics: +/// only M/D/N/=/X operations advance the reference position, while I/S/H/P +/// **Qualimap compatibility note:** Qualimap's Java code advances the reference +/// offset for **all** CIGAR operations, including insertions and soft-clips. +/// This is technically incorrect (I/S consume only query, not reference), but +/// we replicate it here to produce identical enclosure results. The effect is +/// that M-blocks following an I or S operation are shifted rightward by the +/// length of the I/S, which can push them past exon boundaries and change +/// the exonic/intronic classification. +fn extract_m_blocks(record: &bam::Record) -> Vec<(i32, i32)> { + let mut blocks = Vec::new(); + let mut ref_pos = record.pos() as i32; // 0-based + + for op in record.cigar().iter() { + match op { + // Qualimap only creates alignment blocks for M (match/mismatch), + // not for = (sequence match) or X (sequence mismatch). + // In Qualimap's getReadIntervals, only CigarOperator.M creates blocks. + Cigar::Match(len) => { + let len = *len as i32; + blocks.push((ref_pos, ref_pos + len)); + ref_pos += len; + } + // Qualimap bug: EQ and X advance offset but don't create blocks. + Cigar::Equal(len) | Cigar::Diff(len) => { + ref_pos += *len as i32; + } + Cigar::Del(len) | Cigar::RefSkip(len) => { + ref_pos += *len as i32; + } + // Qualimap bug: insertions and soft-clips advance the reference + // position even though they only consume query bases. + Cigar::Ins(len) | Cigar::SoftClip(len) => { + ref_pos += *len as i32; + } + // Qualimap bug: hard clips and pads also advance the reference + // offset even though they shouldn't consume reference bases. + Cigar::HardClip(len) | Cigar::Pad(len) => { + ref_pos += *len as i32; + } + } + } + + blocks +} + +/// Extract junction motifs from N-operations in CIGAR. +/// +/// For each N (intron/RefSkip) operation, extracts the 2bp donor and 2bp acceptor +/// motifs from the read sequence at the junction boundaries. +/// Returns `(n_op_count, motifs)` where `n_op_count` is the total number of +/// N-operations in the CIGAR (used for `reads_at_junctions`), and `motifs` +/// contains the successfully extracted junction motifs. Qualimap counts +/// `numReadsWithJunction` for every N-operation regardless of whether the +/// motif could be extracted. +#[allow(clippy::needless_range_loop, unused_assignments, unused_variables)] +fn extract_junction_motifs(record: &bam::Record) -> (usize, Vec) { + let cigar = record.cigar(); + let seq = record.seq(); + let seq_len = seq.len(); + + let mut motifs = Vec::new(); + let mut n_op_count: usize = 0; + // ref_pos and seq_pos track the current position through the CIGAR. The + // final assignment in the last CIGAR operation is intentionally unused. + let mut ref_pos = record.pos() as i32; + let mut seq_pos: usize = 0; + + for op in cigar.iter() { + match op { + Cigar::Match(len) | Cigar::Equal(len) | Cigar::Diff(len) => { + let len = *len as usize; + ref_pos += len as i32; + seq_pos += len; + } + Cigar::RefSkip(len) => { + // Qualimap increments numReadsWithJunction for every N-op, + // regardless of whether the motif can be extracted. + n_op_count += 1; + + // Extract donor motif: 2bp at end of preceding exon in read + // Extract acceptor motif: 2bp at start of next exon in read + if seq_pos >= 2 && seq_pos + 1 < seq_len { + let donor = [seq.encoded_base(seq_pos - 2), seq.encoded_base(seq_pos - 1)]; + let acceptor = [seq.encoded_base(seq_pos), seq.encoded_base(seq_pos + 1)]; + + // Convert 4-bit encoding to ASCII + let donor_ascii = [decode_base(donor[0]), decode_base(donor[1])]; + let acceptor_ascii = [decode_base(acceptor[0]), decode_base(acceptor[1])]; + + motifs.push(JunctionMotif { + donor: donor_ascii, + acceptor: acceptor_ascii, + }); + } + + ref_pos += *len as i32; + } + Cigar::Ins(len) | Cigar::SoftClip(len) => { + seq_pos += *len as usize; + } + Cigar::Del(len) => { + ref_pos += *len as i32; + } + Cigar::HardClip(_) | Cigar::Pad(_) => {} + } + } + + (n_op_count, motifs) +} + +/// Decode a 4-bit encoded base to ASCII uppercase. +fn decode_base(encoded: u8) -> u8 { + match encoded { + 1 => b'A', + 2 => b'C', + 4 => b'G', + 8 => b'T', + 15 => b'N', + _ => b'N', + } +} + +/// Check whether any cached block hit has an overlap that is not fully enclosed. +/// +/// Pure predicate — does not modify any counters. Used in `reconcile_pair` to +/// avoid double-incrementing `overlapping_exon` when checking both mates. +fn check_has_overlap_not_enclosed(cached_hits: &[CachedBlockHits]) -> bool { + cached_hits.iter().any(|h| h.has_overlap_not_enclosed) +} + +/// Query the merged exon tree ONCE per M-block and cache the results. +/// +/// This single tree query per block replaces the 4+ separate queries that were +/// previously done in `find_enclosing_genes`, `add_per_block_coverage`, +/// `check_overlapping_exon`, and `count_ssp_for_blocks`. +fn cache_block_hits( + m_blocks: &[(i32, i32)], + chrom: &str, + index: &QualimapIndex, +) -> Vec { + let tree = match index.merged_exon_tree(chrom) { + Some(t) => t, + None => { + return m_blocks + .iter() + .map(|_| CachedBlockHits { + enclosing_genes: Vec::new(), + has_overlap_not_enclosed: false, + }) + .collect(); + } + }; + + m_blocks + .iter() + .map(|&(block_start, block_end)| { + let mut enclosing_genes: Vec<(u32, u8)> = Vec::new(); + let mut has_overlap_not_enclosed = false; + + tree.query(block_start, block_end, |iv| { + let exon_start = iv.metadata.exon_start; + let exon_end = iv.metadata.exon_end; + + // Verify actual overlap in half-open coordinates + if exon_start >= block_end || block_start >= exon_end { + return; // Abutting or non-overlapping — skip + } + + // Check enclosure + if block_start >= exon_start && block_end <= exon_end { + let gene_idx = iv.metadata.gene_idx; + let strand = iv.metadata.strand; + // Deduplicate by gene_idx (a gene can have multiple + // merged exons enclosing the same block) + if !enclosing_genes.iter().any(|(g, _)| *g == gene_idx) { + enclosing_genes.push((gene_idx, strand)); + } + } else { + // Overlaps but does NOT enclose + has_overlap_not_enclosed = true; + } + }); + + CachedBlockHits { + enclosing_genes, + has_overlap_not_enclosed, + } + }) + .collect() +} + +/// Find genes whose merged exons enclose ALL M-blocks of a read, using cached hits. +/// +/// Operates on pre-computed `CachedBlockHits` (which store `(gene_idx, strand)` +/// tuples) instead of querying the tree directly. A gene must enclose every +/// M-block and pass the strand filter to be included. +fn find_enclosing_genes_cached( + cached_hits: &[CachedBlockHits], + stranded: u8, + is_reverse: bool, + is_first_of_pair: bool, +) -> HashSet { + if cached_hits.is_empty() { + return HashSet::new(); + } + + // Compute the effective strand of this read after protocol correction. + // Qualimap's getReadIntervals() flips the strand of: + // - read1 for strand-specific-reverse (stranded=2) + // - read2 for strand-specific-forward (stranded=1) + let read_on_plus = if stranded == 0 { + true // no filtering; handled by skipping strand check below + } else { + let flip = (stranded == 2 && is_first_of_pair) || (stranded == 1 && !is_first_of_pair); + if flip { + is_reverse + } else { + !is_reverse + } + }; + + // Closure: does a gene's strand match this read? + let strand_ok = |gene_strand: u8| -> bool { + if stranded == 0 { + return true; + } + (read_on_plus && gene_strand == b'+') || (!read_on_plus && gene_strand == b'-') + }; + + // First M-block: seed candidates from strand-compatible enclosing genes + let mut candidate_genes: HashSet = cached_hits[0] + .enclosing_genes + .iter() + .filter(|(_, strand)| strand_ok(*strand)) + .map(|(gidx, _)| *gidx) + .collect(); + + if candidate_genes.is_empty() { + return candidate_genes; + } + + // Subsequent M-blocks: intersect — keep only genes that enclose every block + for hit in &cached_hits[1..] { + candidate_genes.retain(|gidx| { + hit.enclosing_genes + .iter() + .any(|(g, strand)| g == gidx && strand_ok(*strand)) + }); + if candidate_genes.is_empty() { + break; + } + } + + candidate_genes +} + +/// Find genes whose merged exons enclose ALL M-blocks of a read (original version). +/// +/// This non-cached version is kept for use in unit tests and the +/// `find_enclosing_genes_empty_chrom` test. +#[cfg(test)] +fn find_enclosing_genes( + m_blocks: &[(i32, i32)], + chrom: &str, + index: &QualimapIndex, + stranded: u8, + is_reverse: bool, + is_first_of_pair: bool, +) -> HashSet { + let cached_hits = cache_block_hits(m_blocks, chrom, index); + find_enclosing_genes_cached(&cached_hits, stranded, is_reverse, is_first_of_pair) +} + +/// Build a mate buffer key from a BAM record. +/// +/// Uses FNV-1a hash of qname + r1-centric ordering of positions. +fn make_mate_key(record: &bam::Record) -> MateKey { + let qname_hash = hash_qname(record.qname()); + let tid = record.tid(); + let pos = record.pos(); + let mate_tid = record.mtid(); + let mate_pos = record.mpos(); + + // Always store with read1 position first for consistent lookup + if tid < mate_tid || (tid == mate_tid && pos <= mate_pos) { + (qname_hash, tid, pos, mate_tid, mate_pos) + } else { + (qname_hash, mate_tid, mate_pos, tid, pos) + } +} + +/// FNV-1a hash of a byte slice (for qname hashing). +fn hash_qname(qname: &[u8]) -> u64 { + let mut hash: u64 = 0xcbf29ce484222325; + for &byte in qname { + hash ^= byte as u64; + hash = hash.wrapping_mul(0x100000001b3); + } + hash +} + +// ============================================================ +// Unit tests +// ============================================================ + +#[cfg(test)] +mod tests { + use super::*; + + #[test] + fn test_hash_qname_deterministic() { + let h1 = hash_qname(b"read1"); + let h2 = hash_qname(b"read1"); + let h3 = hash_qname(b"read2"); + assert_eq!(h1, h2); + assert_ne!(h1, h3); + } + + #[test] + fn test_decode_base() { + assert_eq!(decode_base(1), b'A'); + assert_eq!(decode_base(2), b'C'); + assert_eq!(decode_base(4), b'G'); + assert_eq!(decode_base(8), b'T'); + assert_eq!(decode_base(15), b'N'); + assert_eq!(decode_base(0), b'N'); + } + + #[test] + fn test_find_enclosing_genes_empty_chrom() { + let genes = indexmap::IndexMap::new(); + let index = QualimapIndex::from_genes(&genes); + let result = find_enclosing_genes(&[(100, 200)], "chr1", &index, 0, false, true); + assert!(result.is_empty()); + } + + #[test] + fn test_counters_merge() { + let mut c1 = QualimapCounters::default(); + c1.primary_alignments = 10; + c1.exonic_reads = 5; + c1.intronic_reads = 3; + + let c2 = QualimapCounters { + primary_alignments: 20, + exonic_reads: 8, + intronic_reads: 4, + ..Default::default() + }; + + c1.merge(&c2); + assert_eq!(c1.primary_alignments, 30); + assert_eq!(c1.exonic_reads, 13); + assert_eq!(c1.intronic_reads, 7); + } + + #[test] + fn test_junction_motif_counts_merge() { + let mut j1 = JunctionMotifCounts::default(); + j1.counts.insert(([b'G', b'T'], [b'A', b'G']), 5); + + let mut j2 = JunctionMotifCounts::default(); + j2.counts.insert(([b'G', b'T'], [b'A', b'G']), 3); + j2.counts.insert(([b'G', b'C'], [b'A', b'G']), 1); + + j1.merge(&j2); + assert_eq!(j1.counts[&([b'G', b'T'], [b'A', b'G'])], 8); + assert_eq!(j1.counts[&([b'G', b'C'], [b'A', b'G'])], 1); + } +} diff --git a/src/rna/qualimap/coverage.rs b/src/rna/qualimap/coverage.rs new file mode 100644 index 0000000..9c1ae02 --- /dev/null +++ b/src/rna/qualimap/coverage.rs @@ -0,0 +1,474 @@ +//! Per-transcript and per-gene coverage tracking for Qualimap RNA-Seq QC. +//! +//! Maintains per-base coverage arrays for both individual transcripts and +//! merged gene models. Qualimap uses Picard's Gene.Transcript model which +//! merges all exons from all isoforms into a single non-redundant exon set +//! per gene. Coverage for bias/profile is tracked on this merged model. + +use std::collections::HashMap; + +use super::index::{MergedGeneModel, TranscriptInfo}; + +// ============================================================ +// Per-transcript coverage accumulator +// ============================================================ + +/// Per-transcript per-base coverage tracker. +/// +/// Stores a sparse map of transcript flat-index → per-base depth array. +/// Coverage is added for ALL transcripts of a gene when a read is assigned. +/// The depth array uses `i32` to allow efficient increment without overflow +/// concerns for typical RNA-Seq depths. +#[derive(Debug, Clone, Default)] +pub struct TranscriptCoverage { + /// Per-base coverage arrays, keyed by flat transcript index in `QualimapIndex.transcripts`. + /// Only transcripts that have been touched (at least one read assigned to their gene) + /// get an entry here. The `Vec` has length = `transcript.length`. + coverage: HashMap>, +} + +impl TranscriptCoverage { + /// Create a new empty coverage tracker. + pub fn new() -> Self { + Self::default() + } + + /// Add coverage for all transcripts of a gene. + /// + /// For each transcript of the gene, maps the read's M-blocks (genomic coordinates, + /// 0-based half-open) to transcript-relative positions and increments the depth array. + /// + /// # Arguments + /// * `gene_idx` - Index of the assigned gene. + /// * `m_blocks` - Read's M-only aligned blocks in 0-based half-open genomic coords. + /// * `transcripts` - Slice of `TranscriptInfo` for this gene (from `QualimapIndex::gene_transcripts`). + /// * `tx_flat_offset` - Flat index offset: the index of the first transcript of this gene + /// in the global transcripts vec. + pub fn add_coverage( + &mut self, + m_blocks: &[(i32, i32)], + transcripts: &[TranscriptInfo], + tx_flat_offset: u32, + ) { + for (local_idx, tx_info) in transcripts.iter().enumerate() { + let flat_idx = tx_flat_offset + local_idx as u32; + let tx_len = tx_info.exonic_length as usize; + if tx_len == 0 { + continue; + } + + // Get or create the depth array for this transcript. + // Length = exonic_length (sum of exon lengths), matching Picard's + // Gene.Transcript which stores coverage in exonic coordinates. + let depth = self + .coverage + .entry(flat_idx) + .or_insert_with(|| vec![0i32; tx_len]); + + // Map each M-block to exonic coordinates. + // For each genomic position in an M-block that falls within an exon, + // compute the exonic offset (position within concatenated exons) + // and increment the depth at that position. + // + // Picard 1.70's Gene.Transcript.addCoverageCounts() has an off-by-one + // bug: `for (pos = startPos; pos < endPos; ...)` uses strict less-than + // with 1-based inclusive coordinates, effectively skipping the last base + // of each alignment block. We replicate this by using `block_end - 1` + // as the effective end (converting from 0-based half-open to exclusive + // of the last base). + for &(block_start, block_end) in m_blocks { + // Replicate Picard off-by-one: skip last base of each M-block. + // In 0-based half-open, block_end is already exclusive, so + // subtracting 1 makes it skip one additional base. + let effective_end = block_end - 1; + // For each exon, compute overlap with this M-block. + // exonic_offset tracks cumulative exonic bases from prior exons. + let mut exonic_offset = 0usize; + for &(exon_start, exon_end) in &tx_info.exons { + let exon_len = (exon_end - exon_start) as usize; + + // Compute overlap between M-block [block_start, effective_end) + // and exon [exon_start, exon_end) (both 0-based half-open) + let overlap_start = block_start.max(exon_start); + let overlap_end = effective_end.min(exon_end); + + if overlap_start < overlap_end { + // This M-block overlaps this exon. + // Map overlap to exonic coordinates: + // rel_start = exonic_offset + (overlap_start - exon_start) + let rel_start = exonic_offset + (overlap_start - exon_start) as usize; + let rel_end = + (exonic_offset + (overlap_end - exon_start) as usize).min(tx_len); + if rel_start < tx_len && rel_start < rel_end { + for d in &mut depth[rel_start..rel_end] { + *d += 1; + } + } + } + + exonic_offset += exon_len; + } + } + } + } + + /// Merge another `TranscriptCoverage` into this one. + /// + /// For transcripts present in both, adds depth arrays element-wise. + /// For transcripts only in `other`, moves them into `self`. + pub fn merge(&mut self, other: TranscriptCoverage) { + for (tx_idx, other_depth) in other.coverage { + let entry = self.coverage.entry(tx_idx); + match entry { + std::collections::hash_map::Entry::Occupied(mut e) => { + let self_depth = e.get_mut(); + for (i, &val) in other_depth.iter().enumerate() { + if i < self_depth.len() { + self_depth[i] += val; + } + } + } + std::collections::hash_map::Entry::Vacant(e) => { + e.insert(other_depth); + } + } + } + } + + /// Get the depth array for a transcript (by flat index). + #[allow(dead_code)] + pub fn get(&self, tx_flat_idx: u32) -> Option<&[i32]> { + self.coverage.get(&tx_flat_idx).map(|v| v.as_slice()) + } + + /// Number of transcripts with coverage data. + #[allow(dead_code)] + pub fn num_transcripts_with_coverage(&self) -> usize { + self.coverage.len() + } + + /// Iterate over all transcripts with coverage data. + pub fn iter(&self) -> impl Iterator { + self.coverage.iter().map(|(&idx, v)| (idx, v.as_slice())) + } + + /// Compute mean coverage for a transcript. + #[allow(dead_code)] + pub fn mean_coverage(&self, tx_flat_idx: u32) -> f64 { + match self.coverage.get(&tx_flat_idx) { + Some(depth) if !depth.is_empty() => { + let sum: i64 = depth.iter().map(|&d| d as i64).sum(); + sum as f64 / depth.len() as f64 + } + _ => 0.0, + } + } +} + +// ============================================================ +// Merged gene coverage accumulator +// ============================================================ + +/// Per-gene per-base coverage tracker using merged gene models. +/// +/// Qualimap (via Picard's Gene.Transcript) merges all exons from all transcripts +/// of a gene into a single non-redundant exon set. Coverage is tracked on this +/// merged model, which is used for bias calculation and coverage profiles. +/// This produces more accurate bias values than per-transcript tracking because +/// coverage from reads mapping to different isoform exons is unified. +#[derive(Debug, Clone, Default)] +pub struct MergedGeneCoverage { + /// Per-base coverage arrays, keyed by gene index. + /// The `Vec` has length = `MergedGeneModel.exonic_length`. + coverage: HashMap>, +} + +impl MergedGeneCoverage { + /// Create a new empty merged gene coverage tracker. + pub fn new() -> Self { + Self::default() + } + + /// Add coverage for a gene using its merged model. + /// + /// Maps read M-blocks (genomic coordinates, 0-based half-open) to positions + /// in the merged exonic coordinate space and increments the depth array. + /// + /// # Arguments + /// * `gene_idx` - Index of the assigned gene. + /// * `m_blocks` - Read's M-only aligned blocks in 0-based half-open genomic coords. + /// * `model` - The merged gene model with non-redundant exon intervals. + pub fn add_coverage( + &mut self, + gene_idx: u32, + m_blocks: &[(i32, i32)], + model: &MergedGeneModel, + ) { + let total_len = model.exonic_length as usize; + if total_len == 0 { + return; + } + + let depth = self + .coverage + .entry(gene_idx) + .or_insert_with(|| vec![0i32; total_len]); + + // Map each M-block to merged exonic coordinates. + // Replicate Picard off-by-one: skip last base of each M-block. + for &(block_start, block_end) in m_blocks { + let effective_end = block_end - 1; + let mut exonic_offset = 0usize; + for &(exon_start, exon_end) in &model.exons { + let exon_len = (exon_end - exon_start) as usize; + + // Compute overlap between M-block and this merged exon + let overlap_start = block_start.max(exon_start); + let overlap_end = effective_end.min(exon_end); + + if overlap_start < overlap_end { + let rel_start = exonic_offset + (overlap_start - exon_start) as usize; + let rel_end = + (exonic_offset + (overlap_end - exon_start) as usize).min(total_len); + if rel_start < total_len && rel_start < rel_end { + for d in &mut depth[rel_start..rel_end] { + *d += 1; + } + } + } + + exonic_offset += exon_len; + } + } + } + + /// Merge another `MergedGeneCoverage` into this one. + /// + /// For genes present in both, adds depth arrays element-wise. + /// For genes only in `other`, moves them into `self`. + #[allow(dead_code)] + pub fn merge(&mut self, other: MergedGeneCoverage) { + for (gene_idx, other_depth) in other.coverage { + let entry = self.coverage.entry(gene_idx); + match entry { + std::collections::hash_map::Entry::Occupied(mut e) => { + let self_depth = e.get_mut(); + for (i, &val) in other_depth.iter().enumerate() { + if i < self_depth.len() { + self_depth[i] += val; + } + } + } + std::collections::hash_map::Entry::Vacant(e) => { + e.insert(other_depth); + } + } + } + } + + /// Get the depth array for a gene (by gene index). + #[allow(dead_code)] + pub fn get(&self, gene_idx: u32) -> Option<&[i32]> { + self.coverage.get(&gene_idx).map(|v| v.as_slice()) + } + + /// Iterate over all genes with coverage data. + #[allow(dead_code)] + pub fn iter(&self) -> impl Iterator { + self.coverage.iter().map(|(&idx, v)| (idx, v.as_slice())) + } + + /// Number of genes that have any coverage recorded. + #[allow(dead_code)] + pub fn num_genes_with_coverage(&self) -> usize { + self.coverage.len() + } +} + +// ============================================================ +// Unit tests +// ============================================================ + +#[cfg(test)] +mod tests { + use super::*; + + fn make_tx_info(start: i32, end: i32) -> TranscriptInfo { + TranscriptInfo { + gene_idx: 0, + transcript_idx: 0, + gene_id: "g1".to_string(), + transcript_id: "t1".to_string(), + chrom: "chr1".to_string(), + start, + end, + strand: '+', + length: (end - start) as u32, + exons: vec![(start, end)], + exonic_length: (end - start) as u32, + } + } + + #[test] + fn test_add_coverage_single_block() { + let mut cov = TranscriptCoverage::new(); + let tx = make_tx_info(100, 200); + // M-block: 120..150 (0-based half-open) + // Picard off-by-one: effective_end = 149, so coverage at 120..149 + cov.add_coverage(&[(120, 150)], &[tx], 0); + + let depth = cov.get(0).unwrap(); + assert_eq!(depth.len(), 100); + // Positions 20..49 (relative) should have depth 1 (off-by-one: 49 not 50) + assert_eq!(depth[19], 0); + assert_eq!(depth[20], 1); + assert_eq!(depth[48], 1); + assert_eq!(depth[49], 0); + } + + #[test] + fn test_add_coverage_clipping() { + let mut cov = TranscriptCoverage::new(); + let tx = make_tx_info(100, 200); + // M-block extends beyond transcript: 180..220 + cov.add_coverage(&[(180, 220)], &[tx], 0); + + let depth = cov.get(0).unwrap(); + // Only 80..100 (relative) should be covered + assert_eq!(depth[79], 0); + assert_eq!(depth[80], 1); + assert_eq!(depth[99], 1); + } + + #[test] + fn test_merge() { + let mut cov1 = TranscriptCoverage::new(); + let tx = make_tx_info(100, 200); + cov1.add_coverage(&[(120, 150)], &[tx.clone()], 0); + + let mut cov2 = TranscriptCoverage::new(); + cov2.add_coverage(&[(130, 160)], &[tx], 0); + + cov1.merge(cov2); + let depth = cov1.get(0).unwrap(); + // 120..130 relative 20..30: depth 1 + assert_eq!(depth[25], 1); + // 130..150 relative 30..50: depth 2 + assert_eq!(depth[35], 2); + // 150..160 relative 50..60: depth 1 + assert_eq!(depth[55], 1); + } + + #[test] + fn test_mean_coverage() { + let mut cov = TranscriptCoverage::new(); + let tx = make_tx_info(0, 10); + // Cover all 10 bases with depth 1 (Picard off-by-one: only 9 bases) + cov.add_coverage(&[(0, 10)], &[tx], 0); + let mean = cov.mean_coverage(0); + // 9 bases out of 10 covered → mean = 0.9 + assert!((mean - 0.9).abs() < 1e-10); + + // Non-existent transcript + assert!((cov.mean_coverage(99) - 0.0).abs() < 1e-10); + } + + // -------------------------------------------------------- + // MergedGeneCoverage tests + // -------------------------------------------------------- + + #[test] + fn test_merged_gene_single_exon() { + let model = MergedGeneModel { + gene_idx: 0, + strand: '+', + exons: vec![(100, 200)], + exonic_length: 100, + }; + let mut cov = MergedGeneCoverage::new(); + // M-block: 120..150, effective_end = 149 (Picard off-by-one) + cov.add_coverage(0, &[(120, 150)], &model); + + let depth = cov.get(0).unwrap(); + assert_eq!(depth.len(), 100); + assert_eq!(depth[19], 0); + assert_eq!(depth[20], 1); + assert_eq!(depth[48], 1); + assert_eq!(depth[49], 0); + } + + #[test] + fn test_merged_gene_two_exons() { + // Gene with two merged exons: (100,200) and (300,400) + // Total exonic length = 200, offset: first exon 0..100, second 100..200 + let model = MergedGeneModel { + gene_idx: 0, + strand: '+', + exons: vec![(100, 200), (300, 400)], + exonic_length: 200, + }; + let mut cov = MergedGeneCoverage::new(); + // M-block in second exon: 310..330 (genomic), effective_end = 329 + // → offset 100 + 10 = 110..129 (exonic, Picard off-by-one) + cov.add_coverage(0, &[(310, 330)], &model); + + let depth = cov.get(0).unwrap(); + assert_eq!(depth.len(), 200); + assert_eq!(depth[109], 0); + assert_eq!(depth[110], 1); + assert_eq!(depth[128], 1); + assert_eq!(depth[129], 0); + } + + #[test] + fn test_merged_gene_overlapping_transcripts() { + // Simulates what happens when two transcripts have overlapping exons: + // tx1: exons (100,200) and (300,400) + // tx2: exons (150,250) and (350,400) + // Merged: (100,250) and (300,400) → total 250 + let model = MergedGeneModel::from_transcripts( + 0, + '+', + &[(100, 200), (300, 400), (150, 250), (350, 400)], + ); + assert_eq!(model.exons, vec![(100, 250), (300, 400)]); + assert_eq!(model.exonic_length, 250); + + let mut cov = MergedGeneCoverage::new(); + // M-block spanning the merged first exon: 180..220, effective_end = 219 + // → offset 80..119 (Picard off-by-one) + cov.add_coverage(0, &[(180, 220)], &model); + + let depth = cov.get(0).unwrap(); + assert_eq!(depth.len(), 250); + assert_eq!(depth[79], 0); + assert_eq!(depth[80], 1); + assert_eq!(depth[118], 1); + assert_eq!(depth[119], 0); + } + + #[test] + fn test_merged_gene_merge() { + let model = MergedGeneModel { + gene_idx: 0, + strand: '+', + exons: vec![(100, 200)], + exonic_length: 100, + }; + + let mut cov1 = MergedGeneCoverage::new(); + cov1.add_coverage(0, &[(120, 150)], &model); + + let mut cov2 = MergedGeneCoverage::new(); + cov2.add_coverage(0, &[(130, 160)], &model); + + cov1.merge(cov2); + let depth = cov1.get(0).unwrap(); + // 120..130 → offset 20..30: depth 1 + assert_eq!(depth[25], 1); + // 130..150 → offset 30..50: depth 2 + assert_eq!(depth[35], 2); + // 150..160 → offset 50..60: depth 1 + assert_eq!(depth[55], 1); + } +} diff --git a/src/rna/qualimap/index.rs b/src/rna/qualimap/index.rs new file mode 100644 index 0000000..21c1a47 --- /dev/null +++ b/src/rna/qualimap/index.rs @@ -0,0 +1,669 @@ +//! Qualimap-compatible annotation index for RNA-Seq QC. +//! +//! Builds per-chromosome COITrees for exon overlap queries and intron interval +//! trees. Each exon node stores its parent gene and transcript, enabling +//! Qualimap's enclosure-based gene assignment (every M-block must be fully +//! enclosed by exons of the same gene). + +use coitrees::{COITree, Interval, IntervalTree}; +use indexmap::IndexMap; +use log::debug; +use std::collections::HashMap; + +use crate::gtf::Gene; + +// ============================================================ +// Exon node metadata stored in the COITree +// ============================================================ + +/// Metadata for a single exon interval in the COITree. +/// +/// Each node represents one exon of one transcript of one gene. +/// Qualimap assigns reads by checking that all M-blocks are *enclosed* +/// (fully contained) within exons of the same gene. +#[derive(Debug, Clone, Copy)] +pub struct ExonMeta { + /// Index into the gene list (position in the IndexMap). + #[allow(dead_code)] + pub gene_idx: u32, + /// Index into the transcript list within the gene. + #[allow(dead_code)] + pub transcript_idx: u16, + /// Exon start in 0-based half-open coordinates. + #[allow(dead_code)] + pub exon_start: i32, + /// Exon end in 0-based half-open coordinates. + #[allow(dead_code)] + pub exon_end: i32, + /// Strand ('+', '-', or '.'). + #[allow(dead_code)] + pub strand: u8, +} + +impl Default for ExonMeta { + fn default() -> Self { + Self { + gene_idx: 0, + transcript_idx: 0, + exon_start: 0, + exon_end: 0, + strand: b'.', + } + } +} + +/// Per-chromosome exon COITree for overlap queries. +pub type ExonTree = COITree; + +// ============================================================ +// Intron node metadata +// ============================================================ + +/// Metadata for an intron interval (gap between consecutive exons of a transcript). +#[derive(Debug, Clone, Copy, Default)] +#[allow(dead_code)] +pub struct IntronMeta { + /// Index into the gene list. + pub gene_idx: u32, +} + +/// Per-chromosome intron COITree for intronic read classification. +pub type IntronTree = COITree; + +// ============================================================ +// Merged exon node metadata +// ============================================================ + +/// Metadata for a merged exon interval in the COITree. +/// +/// Qualimap Java merges overlapping/abutting exons per gene before building +/// its IntervalTree. This merged representation is used for the enclosure +/// check (gene assignment). A read block enclosed by a merged interval is +/// considered "exonic" even if no single transcript exon fully contains it. +#[derive(Debug, Clone, Copy)] +pub struct MergedExonMeta { + /// Index into the gene list (position in the IndexMap). + pub gene_idx: u32, + /// Exon start in 0-based half-open coordinates. + pub exon_start: i32, + /// Exon end in 0-based half-open coordinates. + pub exon_end: i32, + /// Strand (b'+', b'-', or b'.'). + pub strand: u8, +} + +impl Default for MergedExonMeta { + fn default() -> Self { + Self { + gene_idx: 0, + exon_start: 0, + exon_end: 0, + strand: b'.', + } + } +} + +/// Per-chromosome merged exon COITree for enclosure-based gene assignment. +/// +/// Uses merged per-gene exon intervals (union of all transcript exons) to match +/// Qualimap Java's interval tree behavior. +pub type MergedExonTree = COITree; + +// ============================================================ +// Per-transcript metadata +// ============================================================ + +/// Pre-computed metadata for a single transcript, used for coverage tracking. +#[derive(Debug, Clone)] +#[allow(dead_code)] +pub struct TranscriptInfo { + /// Gene index (position in the IndexMap). + pub gene_idx: u32, + /// Transcript index within the gene. + pub transcript_idx: u16, + /// Gene ID string (for output). + pub gene_id: String, + /// Transcript ID string. + pub transcript_id: String, + /// Chromosome name. + pub chrom: String, + /// Transcript start (0-based). + pub start: i32, + /// Transcript end (0-based half-open). + pub end: i32, + /// Strand. + pub strand: char, + /// Total transcript length (end - start). + pub length: u32, + /// Sorted exon intervals in 0-based half-open coordinates. + pub exons: Vec<(i32, i32)>, + /// Total exonic bases (sum of exon lengths). + pub exonic_length: u32, +} + +// ============================================================ +// Merged gene model — union of all transcript exons per gene +// ============================================================ + +/// Merged exon model for a gene: union of all exons across all transcripts. +/// +/// Qualimap (via Picard's `Gene.Transcript`) merges all exons from all isoforms +/// into a single non-redundant exon set per gene. Coverage is tracked on this +/// merged model, which gives the correct bias and coverage profile values. +#[derive(Debug, Clone)] +pub struct MergedGeneModel { + /// Gene index (position in the IndexMap). + #[allow(dead_code)] + pub gene_idx: u32, + /// Strand ('+', '-', or '.'). + #[allow(dead_code)] + pub strand: char, + /// Merged non-overlapping exon intervals in 0-based half-open coordinates, sorted by start. + pub exons: Vec<(i32, i32)>, + /// Total merged exonic length (sum of merged exon lengths). + pub exonic_length: u32, +} + +impl MergedGeneModel { + /// Build a merged gene model from all transcripts of a gene. + /// + /// Takes all exon intervals (0-based half-open) from all transcripts, + /// sorts them, and merges overlapping/adjacent intervals into a single + /// non-redundant set. + pub fn from_transcripts(gene_idx: u32, strand: char, all_exons: &[(i32, i32)]) -> Self { + let exons = merge_intervals(all_exons); + let exonic_length: u32 = exons.iter().map(|(s, e)| (e - s) as u32).sum(); + Self { + gene_idx, + strand, + exons, + exonic_length, + } + } +} + +/// Merge overlapping and adjacent intervals into non-redundant sorted intervals. +/// +/// Input: arbitrary list of (start, end) 0-based half-open intervals. +/// Output: sorted, non-overlapping intervals where overlapping/touching intervals +/// have been merged. +fn merge_intervals(intervals: &[(i32, i32)]) -> Vec<(i32, i32)> { + if intervals.is_empty() { + return Vec::new(); + } + let mut sorted: Vec<(i32, i32)> = intervals.to_vec(); + sorted.sort_unstable_by_key(|(s, _)| *s); + + let mut merged = Vec::with_capacity(sorted.len()); + let (mut cur_start, mut cur_end) = sorted[0]; + + for &(start, end) in &sorted[1..] { + if start <= cur_end { + // Overlapping or abutting — extend (matches Qualimap's intersects() || abuts()) + cur_end = cur_end.max(end); + } else { + // Gap — emit current and start new + merged.push((cur_start, cur_end)); + cur_start = start; + cur_end = end; + } + } + merged.push((cur_start, cur_end)); + merged +} + +// ============================================================ +// QualimapIndex — the main index structure +// ============================================================ + +/// Complete Qualimap annotation index built from GTF genes. +/// +/// Contains per-chromosome exon and intron trees, plus transcript metadata +/// and merged gene models for coverage tracking. +/// This index is *separate* from the existing dupRadar/featureCounts index +/// because Qualimap uses fundamentally different assignment logic. +pub struct QualimapIndex { + /// Per-chromosome exon COITrees (key = chromosome name). + /// Individual per-transcript exons — used for coverage tracking. + pub exon_trees: HashMap, + /// Per-chromosome merged exon COITrees (key = chromosome name). + /// Merged per-gene exons — used for enclosure-based gene assignment. + /// Matches Qualimap Java's `GenomicRegionSet.addRegion()` which merges + /// overlapping/abutting exons per gene via `concatenateIntervals()`. + pub merged_exon_trees: HashMap, + /// Per-chromosome intron COITrees (key = chromosome name). + pub intron_trees: HashMap, + /// All transcript metadata, indexed by a flat transcript ID. + /// The index is `(gene_idx, transcript_idx)` mapped to a flat position. + pub transcripts: Vec, + /// Lookup: gene_idx -> range of transcript indices in `transcripts` vec. + /// `gene_transcript_ranges[gene_idx] = (start, end)` half-open into `transcripts`. + pub gene_transcript_ranges: Vec<(u32, u32)>, + /// Merged gene models: one per gene, indexed by gene_idx. + /// Each merges all exons from all transcripts into non-redundant intervals. + pub merged_gene_models: Vec, + /// Total number of genes. + #[allow(dead_code)] + pub num_genes: u32, +} + +impl QualimapIndex { + /// Build the Qualimap index from GTF gene annotations. + /// + /// Creates per-chromosome exon COITrees (with enclosure metadata) and intron + /// interval trees. Also builds per-transcript metadata for coverage tracking. + /// + /// # Arguments + /// * `genes` - Gene annotations from GTF parsing (insertion-order preserved). + pub fn from_genes(genes: &IndexMap) -> Self { + // Collect exon intervals and intron intervals per chromosome + let mut exon_intervals: HashMap>> = HashMap::new(); + let mut intron_intervals: HashMap>> = HashMap::new(); + let mut transcripts = Vec::new(); + let mut gene_transcript_ranges = Vec::with_capacity(genes.len()); + + let mut merged_gene_models = Vec::with_capacity(genes.len()); + + for (gene_idx, gene) in genes.values().enumerate() { + let gene_idx = gene_idx as u32; + let tx_start_idx = transcripts.len() as u32; + + // Collect all exons from all transcripts for merged gene model + let mut all_gene_exons: Vec<(i32, i32)> = Vec::new(); + + for (tx_idx, tx) in gene.transcripts.iter().enumerate() { + let tx_idx = tx_idx as u16; + + // Convert transcript exons from 1-based inclusive (GTF) to 0-based half-open + let mut exons_0based: Vec<(i32, i32)> = tx + .exons + .iter() + .map(|(s, e)| ((*s as i32) - 1, *e as i32)) + .collect(); + exons_0based.sort_unstable_by_key(|(s, _)| *s); + + let exonic_length: u32 = exons_0based.iter().map(|(s, e)| (e - s) as u32).sum(); + + let tx_start = exons_0based.first().map(|(s, _)| *s).unwrap_or(0); + let tx_end = exons_0based.last().map(|(_, e)| *e).unwrap_or(0); + + // Collect for merged gene model + all_gene_exons.extend_from_slice(&exons_0based); + + // Add exon intervals to the per-chrom collection + let chrom_exons = exon_intervals.entry(tx.chrom.clone()).or_default(); + for &(start, end) in &exons_0based { + chrom_exons.push(Interval::new( + start, + end, + ExonMeta { + gene_idx, + transcript_idx: tx_idx, + exon_start: start, + exon_end: end, + strand: tx.strand as u8, + }, + )); + } + + // Add intron intervals (gaps between consecutive exons) + let chrom_introns = intron_intervals.entry(tx.chrom.clone()).or_default(); + for window in exons_0based.windows(2) { + let intron_start = window[0].1; + let intron_end = window[1].0; + if intron_end > intron_start { + chrom_introns.push(Interval::new( + intron_start, + intron_end, + IntronMeta { gene_idx }, + )); + } + } + + // Qualimap Java's createHelperMaps() sorts negative-strand exons in + // descending order by start position (Arrays.sort with comparator + // `e1.start > e2.start ? -1 : 1`). This in-place mutation affects + // getTranscriptCoordinate() during BAM processing: for minus-strand + // transcripts, position 0 in the coverage array corresponds to the + // rightmost exon (biological 5' end). We replicate this here by + // re-sorting minus-strand exons descending after the ascending-order + // work (interval tree, intron gaps) is done. + let coverage_exons = if tx.strand == '-' { + let mut desc = exons_0based.clone(); + desc.sort_unstable_by(|a, b| b.0.cmp(&a.0)); + desc + } else { + exons_0based + }; + + // Store transcript metadata + transcripts.push(TranscriptInfo { + gene_idx, + transcript_idx: tx_idx, + gene_id: gene.gene_id.clone(), + transcript_id: tx.transcript_id.clone(), + chrom: tx.chrom.clone(), + start: tx_start, + end: tx_end, + strand: tx.strand, + length: (tx_end - tx_start) as u32, + exons: coverage_exons, + exonic_length, + }); + } + + let tx_end_idx = transcripts.len() as u32; + gene_transcript_ranges.push((tx_start_idx, tx_end_idx)); + + // Build merged gene model from all exons across all transcripts + merged_gene_models.push(MergedGeneModel::from_transcripts( + gene_idx, + gene.strand, + &all_gene_exons, + )); + } + + // Build merged exon intervals from merged gene models. + // Qualimap Java merges overlapping/abutting exons per gene before inserting + // them into its IntervalTree. We build a separate COITree from these merged + // intervals for the enclosure-based gene assignment check. + let mut merged_exon_intervals: HashMap>> = + HashMap::new(); + for (gene_idx_usize, gene) in genes.values().enumerate() { + let gene_idx = gene_idx_usize as u32; + let model = &merged_gene_models[gene_idx_usize]; + // Use the first transcript's chromosome (all transcripts of a gene share the same chrom) + if let Some(tx) = gene.transcripts.first() { + let chrom_merged = merged_exon_intervals.entry(tx.chrom.clone()).or_default(); + for &(start, end) in &model.exons { + chrom_merged.push(Interval::new( + start, + end, + MergedExonMeta { + gene_idx, + exon_start: start, + exon_end: end, + strand: model.strand as u8, + }, + )); + } + } + } + + // Build COITrees from collected intervals + let total_exon_ivs: usize = exon_intervals.values().map(|v| v.len()).sum(); + let total_merged_ivs: usize = merged_exon_intervals.values().map(|v| v.len()).sum(); + log::info!( + "QM_INDEX: {} exon intervals ({} merged), {} transcripts, {} genes", + total_exon_ivs, + total_merged_ivs, + transcripts.len(), + gene_transcript_ranges.len() + ); + let exon_trees: HashMap = exon_intervals + .into_iter() + .map(|(chrom, intervals)| (chrom, COITree::new(&intervals))) + .collect(); + + let merged_exon_trees: HashMap = merged_exon_intervals + .into_iter() + .map(|(chrom, intervals)| (chrom, COITree::new(&intervals))) + .collect(); + + let intron_trees: HashMap = intron_intervals + .into_iter() + .map(|(chrom, intervals)| (chrom, COITree::new(&intervals))) + .collect(); + + let num_genes = genes.len() as u32; + + debug!( + "Built Qualimap index: {} genes, {} transcripts, {} chromosomes with exons", + num_genes, + transcripts.len(), + exon_trees.len(), + ); + + Self { + exon_trees, + merged_exon_trees, + intron_trees, + transcripts, + gene_transcript_ranges, + merged_gene_models, + num_genes, + } + } + + /// Get the per-transcript exon tree for a chromosome (used for coverage tracking). + #[allow(dead_code)] + pub fn exon_tree(&self, chrom: &str) -> Option<&ExonTree> { + self.exon_trees.get(chrom) + } + + /// Get the merged exon tree for a chromosome (used for enclosure-based gene assignment). + /// + /// Qualimap Java merges overlapping/abutting exons per gene before checking + /// enclosure. This tree contains those merged intervals, ensuring reads that + /// span two overlapping transcript exons of the same gene are correctly + /// classified as "exonic". + pub fn merged_exon_tree(&self, chrom: &str) -> Option<&MergedExonTree> { + self.merged_exon_trees.get(chrom) + } + + /// Get the intron tree for a chromosome. + pub fn intron_tree(&self, chrom: &str) -> Option<&IntronTree> { + self.intron_trees.get(chrom) + } + + /// Get transcript info entries for a gene by gene index. + /// + /// Returns a slice of `TranscriptInfo` for all transcripts of the gene. + pub fn gene_transcripts(&self, gene_idx: u32) -> &[TranscriptInfo] { + let (start, end) = self.gene_transcript_ranges[gene_idx as usize]; + &self.transcripts[start as usize..end as usize] + } +} + +// ============================================================ +// Unit tests +// ============================================================ + +#[cfg(test)] +mod tests { + use super::*; + use crate::gtf::{Exon, Gene, Transcript}; + + /// Helper to build a minimal gene for testing. + fn make_gene(gene_id: &str, chrom: &str, strand: char, transcripts: Vec) -> Gene { + let start = transcripts + .iter() + .flat_map(|t| t.exons.iter().map(|(s, _)| *s)) + .min() + .unwrap_or(1); + let end = transcripts + .iter() + .flat_map(|t| t.exons.iter().map(|(_, e)| *e)) + .max() + .unwrap_or(1); + let exons = transcripts + .iter() + .flat_map(|t| { + t.exons.iter().map(|(s, e)| Exon { + chrom: chrom.to_string(), + start: *s, + end: *e, + strand, + }) + }) + .collect(); + Gene { + gene_id: gene_id.to_string(), + chrom: chrom.to_string(), + start, + end, + strand, + exons, + effective_length: 0, + attributes: HashMap::new(), + transcripts, + } + } + + fn make_transcript( + tx_id: &str, + chrom: &str, + strand: char, + exons: Vec<(u64, u64)>, + ) -> Transcript { + let start = exons.iter().map(|(s, _)| *s).min().unwrap_or(1); + let end = exons.iter().map(|(_, e)| *e).max().unwrap_or(1); + Transcript { + transcript_id: tx_id.to_string(), + chrom: chrom.to_string(), + start, + end, + strand, + exons, + cds_start: None, + cds_end: None, + } + } + + #[test] + fn test_index_from_single_gene() { + let mut genes = IndexMap::new(); + let tx = make_transcript("tx1", "chr1", '+', vec![(101, 200), (301, 400)]); + let gene = make_gene("gene1", "chr1", '+', vec![tx]); + genes.insert("gene1".to_string(), gene); + + let index = QualimapIndex::from_genes(&genes); + + assert_eq!(index.num_genes, 1); + assert_eq!(index.transcripts.len(), 1); + assert!(index.exon_tree("chr1").is_some()); + assert!(index.intron_tree("chr1").is_some()); + assert!(index.exon_tree("chr2").is_none()); + + // Check transcript metadata + let ti = &index.transcripts[0]; + assert_eq!(ti.gene_id, "gene1"); + assert_eq!(ti.transcript_id, "tx1"); + assert_eq!(ti.exons.len(), 2); + // GTF 1-based inclusive (101, 200) -> 0-based half-open (100, 200) + assert_eq!(ti.exons[0], (100, 200)); + // GTF 1-based inclusive (301, 400) -> 0-based half-open (300, 400) + assert_eq!(ti.exons[1], (300, 400)); + assert_eq!(ti.exonic_length, 200); // 100 + 100 + + // Check gene transcript ranges + let txs = index.gene_transcripts(0); + assert_eq!(txs.len(), 1); + assert_eq!(txs[0].transcript_id, "tx1"); + + // Check that exon tree has entries + let tree = index.exon_tree("chr1").unwrap(); + let mut hits = Vec::new(); + tree.query(150, 160, |iv| hits.push(iv.metadata.clone())); + assert_eq!(hits.len(), 1); + assert_eq!(hits[0].gene_idx, 0); + + // Check intron tree: intron from 200..300 + let itree = index.intron_tree("chr1").unwrap(); + let mut ihits = Vec::new(); + itree.query(250, 260, |iv| ihits.push(iv.metadata.clone())); + assert_eq!(ihits.len(), 1); + assert_eq!(ihits[0].gene_idx, 0); + } + + #[test] + fn test_index_multiple_transcripts() { + let mut genes = IndexMap::new(); + let tx1 = make_transcript("tx1", "chr1", '+', vec![(101, 200), (301, 400)]); + let tx2 = make_transcript("tx2", "chr1", '+', vec![(101, 250), (351, 400)]); + let gene = make_gene("gene1", "chr1", '+', vec![tx1, tx2]); + genes.insert("gene1".to_string(), gene); + + let index = QualimapIndex::from_genes(&genes); + + assert_eq!(index.transcripts.len(), 2); + let txs = index.gene_transcripts(0); + assert_eq!(txs.len(), 2); + assert_eq!(txs[0].transcript_id, "tx1"); + assert_eq!(txs[1].transcript_id, "tx2"); + } + + #[test] + fn test_enclosure_check() { + // Simulate what the accumulator will do: check if an M-block + // is fully enclosed within any single exon of a gene. + let mut genes = IndexMap::new(); + let tx = make_transcript("tx1", "chr1", '+', vec![(101, 200), (301, 400)]); + let gene = make_gene("gene1", "chr1", '+', vec![tx]); + genes.insert("gene1".to_string(), gene); + + let index = QualimapIndex::from_genes(&genes); + let tree = index.exon_tree("chr1").unwrap(); + + // M-block 120..180 (0-based) should be enclosed by exon (100, 200) + let mut enclosed_genes = Vec::new(); + tree.query(120, 180, |iv| { + if 120 >= iv.metadata.exon_start && 180 <= iv.metadata.exon_end { + enclosed_genes.push(iv.metadata.gene_idx); + } + }); + assert_eq!(enclosed_genes, vec![0]); + + // M-block 190..310 (0-based) overlaps both exons but is NOT enclosed by either + let mut enclosed_genes2 = Vec::new(); + tree.query(190, 310, |iv| { + if 190 >= iv.metadata.exon_start && 310 <= iv.metadata.exon_end { + enclosed_genes2.push(iv.metadata.gene_idx); + } + }); + assert!(enclosed_genes2.is_empty()); + } + + #[test] + fn test_merged_exon_enclosure() { + // Qualimap Java merges overlapping/abutting exons per gene before + // building the interval tree. A read block that spans two overlapping + // transcript exons is enclosed by the merged interval but NOT by + // either individual exon. + let mut genes = IndexMap::new(); + // tx1: exon [100, 200), tx2: exon [150, 300) → merged: [100, 300) + let tx1 = make_transcript("tx1", "chr1", '+', vec![(101, 200)]); + let tx2 = make_transcript("tx2", "chr1", '+', vec![(151, 300)]); + let gene = make_gene("gene1", "chr1", '+', vec![tx1, tx2]); + genes.insert("gene1".to_string(), gene); + + let index = QualimapIndex::from_genes(&genes); + + // Block [120, 250) is NOT enclosed by either individual exon + let per_tx_tree = index.exon_tree("chr1").unwrap(); + let mut per_tx_enclosed = Vec::new(); + per_tx_tree.query(120, 250, |iv| { + if 120 >= iv.metadata.exon_start && 250 <= iv.metadata.exon_end { + per_tx_enclosed.push(iv.metadata.gene_idx); + } + }); + assert!( + per_tx_enclosed.is_empty(), + "Block should NOT be enclosed by any individual transcript exon" + ); + + // But it IS enclosed by the merged exon [100, 300) + let merged_tree = index.merged_exon_tree("chr1").unwrap(); + let mut merged_enclosed = Vec::new(); + merged_tree.query(120, 250, |iv| { + if 120 >= iv.metadata.exon_start && 250 <= iv.metadata.exon_end { + merged_enclosed.push(iv.metadata.gene_idx); + } + }); + assert_eq!( + merged_enclosed, + vec![0], + "Block should be enclosed by merged exon interval" + ); + } +} diff --git a/src/rna/qualimap/mod.rs b/src/rna/qualimap/mod.rs new file mode 100644 index 0000000..374767e --- /dev/null +++ b/src/rna/qualimap/mod.rs @@ -0,0 +1,92 @@ +//! Qualimap RNA-Seq QC module. +//! +//! Reimplements Qualimap's RNA-Seq quality control analysis with enclosure-based +//! gene assignment, per-transcript coverage tracking, and Qualimap-compatible output. + +pub mod accumulator; +pub mod coverage; +pub mod index; +pub mod output; + +pub use accumulator::QualimapAccum; +pub use index::QualimapIndex; + +use std::collections::HashMap; + +// ============================================================================ +// Result types +// ============================================================================ + +/// Final Qualimap result, produced from a merged `QualimapAccum`. +/// +/// Holds all counters and coverage data needed to produce Qualimap-compatible +/// output files (coverage profiles, bias metrics, `rnaseq_qc_results.txt`). +#[derive(Debug)] +pub struct QualimapResult { + // --- Read counters --- + /// Total primary alignments (excluding unmapped, secondary, supplementary, QC-fail). + pub primary_alignments: u64, + /// Total secondary alignments seen. + pub secondary_alignments: u64, + /// Reads skipped because they were not aligned. + pub not_aligned: u64, + /// Reads skipped because NH > 1 (multi-mappers). + pub alignment_not_unique: u64, + + // --- Gene assignment counters --- + /// Reads assigned to exactly one gene (exonic). + pub exonic_reads: u64, + /// Reads where >1 gene encloses all blocks (ambiguous). + pub ambiguous_reads: u64, + /// Reads with no gene enclosing all blocks. + pub no_feature: u64, + /// Reads classified as intronic (M-block overlaps intron tree). + pub intronic_reads: u64, + /// Reads classified as intergenic (no exon or intron overlap). + pub intergenic_reads: u64, + /// Reads overlapping exons from multiple genes. + pub overlapping_exon_reads: u64, + + // --- Fragment counters (PE) --- + /// Total reads counted (PE: each mate counts as 1 read). + pub read_count: u64, + /// Total fragments counted (PE: 1 per paired fragment). + #[allow(dead_code)] // populated but not yet consumed in output + pub fragment_count: u64, + /// Left-of-pair reads (first-of-pair in paired mode). + pub left_proper_in_pair: u64, + /// Right-of-pair reads (second-of-pair in paired mode). + pub right_proper_in_pair: u64, + /// Both mates with proper-pair flag (for numberOfMappedPairs = count / 2). + pub both_proper_in_pair: u64, + + // --- Junction counters --- + /// Reads containing at least one splice junction (N-op in CIGAR). + pub reads_at_junctions: u64, + /// Junction motif counts: canonical_motif_string -> count. + pub junction_motifs: HashMap, + + // --- Per-transcript coverage --- + /// Per-transcript coverage arrays (transcript_key -> per-base coverage). + #[allow(dead_code)] // populated but not yet consumed in output + pub transcript_coverage: HashMap>, + + /// Raw per-transcript coverage keyed by flat index (for bias computation). + /// Retains the internal indexing used during accumulation so that bias + /// computation can look up transcript metadata (strand, exonic length) + /// efficiently via the `QualimapIndex`. + pub transcript_coverage_raw: coverage::TranscriptCoverage, + + // --- Merged gene coverage --- + /// Per-gene coverage using merged exon models (gene_idx -> per-base coverage). + /// Qualimap's Picard Gene.Transcript merges all exons from all isoforms into + /// a single non-redundant exon set per gene. This produces more accurate + /// bias and profile values than per-transcript tracking. + #[allow(dead_code)] // populated but not yet consumed in output + pub merged_gene_coverage: coverage::MergedGeneCoverage, + + /// Forward strand estimation count for SSP. + pub ssp_fwd: u64, + /// Reverse strand estimation count for SSP. + pub ssp_rev: u64, +} diff --git a/src/rna/qualimap/output.rs b/src/rna/qualimap/output.rs new file mode 100644 index 0000000..b00b0af --- /dev/null +++ b/src/rna/qualimap/output.rs @@ -0,0 +1,807 @@ +//! Qualimap RNA-Seq QC output generation. +//! +//! Produces `rnaseq_qc_results.txt` and coverage profile TSVs in exact +//! Qualimap-compatible format, parseable by MultiQC. + +use std::io::Write; +use std::path::Path; + +use anyhow::{Context, Result}; +use log::info; + +use super::coverage::TranscriptCoverage; +use super::index::QualimapIndex; +use super::QualimapResult; + +// ============================= Constants ======================================= + +/// Number of percentile bins for coverage profiles. +const NUM_BINS: usize = 100; + +/// Number of transcripts for the "high" expression tier. +const HIGH_TIER_COUNT: usize = 500; + +/// Number of transcripts for the "low" expression tier. +const LOW_TIER_COUNT: usize = 500; + +/// Number of top transcripts used for 5'-3' bias calculation. +const NUM_TRANSCRIPTS_FOR_BIAS: usize = 1000; + +/// Number of bases at 5'/3' ends used for bias calculation. +const NUM_PRIME_BASES: usize = 100; + +/// Minimum transcript length for bias calculation. +const MIN_TRANSCRIPT_LENGTH_FOR_BIAS: usize = 500; + +// ============================= Number Formatting =============================== + +/// Format an integer with comma separators (e.g., 1234567 → "1,234,567"). +fn format_with_commas(n: u64) -> String { + let s = n.to_string(); + let bytes = s.as_bytes(); + let len = bytes.len(); + if len <= 3 { + return s; + } + let mut result = String::with_capacity(len + (len - 1) / 3); + for (i, &b) in bytes.iter().enumerate() { + if i > 0 && (len - i).is_multiple_of(3) { + result.push(','); + } + result.push(b as char); + } + result +} + +/// Format a percentage with Qualimap-style precision. +/// +/// Qualimap uses Java's default `String.format("%.2f", val)` but with +/// trailing-zero trimming on the decimal part. Looking at real output: +/// - 68.3% (not 68.30%) +/// - 29.69% +/// - 2.01% +/// - 9.31% +/// +/// The pattern is: 2 decimal places, then strip trailing zeros (but keep +/// at least one decimal digit). +fn format_percentage(val: f64) -> String { + let s = format!("{:.2}", val); + // Strip trailing zeros after decimal point, but keep at least one decimal + if s.contains('.') { + let trimmed = s.trim_end_matches('0'); + let trimmed = if trimmed.ends_with('.') { + // e.g., "68." → keep at least "68.0" + // Actually Qualimap shows "68.3" not "68.0" — but if we get exactly + // an integer like 68.00, it would show "68.0" based on the trim logic. + // However looking at real data, Qualimap never shows ".0" — it shows + // integers as "68" etc. Let's check: the real data shows "68.3%", "29.69%" + // etc. When the value is exactly integer, Qualimap shows e.g. "9.31%". + // There's no case of exactly-integer percentages in the reference. + // Be safe: keep "X.0" format. + &s[..trimmed.len() + 1] + } else { + trimmed + }; + trimmed.to_string() + } else { + s + } +} + +/// Format a bias value with Qualimap-style precision. +/// +/// Qualimap uses 2 decimal places with trailing-zero trimming. +/// Examples: 0.71, 0.57, 1.3, 1.47, 0.31, 0.22 +fn format_bias(val: f64) -> String { + let s = format!("{:.2}", val); + if s.contains('.') { + let trimmed = s.trim_end_matches('0'); + if trimmed.ends_with('.') { + format!("{}.0", trimmed.trim_end_matches('.')) + } else { + trimmed.to_string() + } + } else { + s + } +} + +// ============================= Coverage Profile ================================ + +/// Per-transcript coverage data used for profile computation. +struct TranscriptCoverageEntry { + /// Per-base depth array. + coverage: Vec, + /// Mean coverage across the array. + mean_coverage: f64, + /// Strand: '+' or '-'. + strand: char, + /// Gene index for best-per-gene selection. + gene_idx: u32, + /// Flat transcript index (for diagnostics). + #[allow(dead_code)] + flat_idx: u32, +} + +/// Compute coverage profiles using Qualimap's GenericHistogram algorithm. +/// +/// For each transcript with mean coverage > 0: +/// 1. Bin the per-base coverage into `NUM_BINS` percentile bins +/// 2. Normalize by transcript length +/// 3. Accumulate across all transcripts +/// +/// Returns a 100-element array of f64 values. +fn compute_coverage_profile(entries: &[&TranscriptCoverageEntry]) -> [f64; NUM_BINS] { + let mut hist = [0.0f64; NUM_BINS]; + + for entry in entries { + let data = &entry.coverage; + let len = data.len(); + if len == 0 { + continue; + } + + // Bin coverage into NUM_BINS (100) bins using step = ceil(len / 100). + // Matches Qualimap's GenericHistogram behavior where each bin accumulates + // coverage from `step` consecutive positions, normalized by transcript length. + let step = len.div_ceil(NUM_BINS).max(1); + let norm = len as f64; + let mut bin = 0; + let mut bin_sum = 0.0f64; + let mut count = 0; + + for (i, &val) in data.iter().enumerate() { + bin_sum += val as f64; + count += 1; + if count == step || i == len - 1 { + hist[bin] += bin_sum / norm; + bin += 1; + bin_sum = 0.0; + count = 0; + } + } + } + + hist +} + +/// Compute 5'-3' bias values from per-transcript coverage. +/// +/// For each qualifying transcript (length >= 500, mean >= 1.0): +/// - Compute mean coverage of first `NUM_PRIME_BASES` bases (5' end) +/// - Compute mean coverage of last `NUM_PRIME_BASES` bases (3' end) +/// - Compute mean coverage of entire transcript +/// - 5' bias = 5' mean / whole mean +/// - 3' bias = 3' mean / whole mean +/// - 5'-3' bias = 5' mean / 3' mean +/// +/// For negative-strand transcripts, the coverage array is reversed before +/// computing 5'/3' regions. +/// +/// Returns (5' bias, 3' bias, 5'-3' bias) as medians across all qualifying +/// transcripts. +fn compute_bias(entries: &[TranscriptCoverageEntry]) -> (f64, f64, f64) { + use std::collections::HashMap; + + // Step 1: Pick best transcript per gene (highest mean coverage). + // Qualimap selects one transcript per gene, then filters by length >= 500 + // and mean >= 1.0, then takes the top 1000 by mean coverage. + let mut best_per_gene: HashMap = HashMap::new(); + for entry in entries { + if entry.coverage.len() < MIN_TRANSCRIPT_LENGTH_FOR_BIAS || entry.mean_coverage < 1.0 { + continue; + } + let gene = entry.gene_idx; + let current_best = best_per_gene.get(&gene); + if current_best.is_none() || entry.mean_coverage > current_best.unwrap().mean_coverage { + best_per_gene.insert(gene, entry); + } + } + + // Collect qualifying transcripts and sort by mean coverage descending + let mut qualifying: Vec<(f64, &TranscriptCoverageEntry)> = best_per_gene + .values() + .map(|e| (e.mean_coverage, *e)) + .collect(); + + if qualifying.is_empty() { + return (f64::NAN, f64::NAN, f64::NAN); + } + + // Sort by mean coverage descending, take top N + qualifying.sort_by(|a, b| b.0.partial_cmp(&a.0).unwrap_or(std::cmp::Ordering::Equal)); + qualifying.truncate(NUM_TRANSCRIPTS_FOR_BIAS); + + let mut five_prime_biases = Vec::with_capacity(qualifying.len()); + let mut three_prime_biases = Vec::with_capacity(qualifying.len()); + let mut five_three_biases = Vec::with_capacity(qualifying.len()); + + for (_, entry) in &qualifying { + let cov = &entry.coverage; + let len = cov.len(); + if len < NUM_PRIME_BASES { + continue; + } + + // For negative strand, reverse the array conceptually + let (five_prime_sum, three_prime_sum, whole_sum) = if entry.strand == '-' { + // 5' end is at the END of the array for negative strand + let five_sum: f64 = cov[len - NUM_PRIME_BASES..].iter().map(|&v| v as f64).sum(); + let three_sum: f64 = cov[..NUM_PRIME_BASES].iter().map(|&v| v as f64).sum(); + let whole_sum: f64 = cov.iter().map(|&v| v as f64).sum(); + (five_sum, three_sum, whole_sum) + } else { + let five_sum: f64 = cov[..NUM_PRIME_BASES].iter().map(|&v| v as f64).sum(); + let three_sum: f64 = cov[len - NUM_PRIME_BASES..].iter().map(|&v| v as f64).sum(); + let whole_sum: f64 = cov.iter().map(|&v| v as f64).sum(); + (five_sum, three_sum, whole_sum) + }; + + let five_mean = five_prime_sum / NUM_PRIME_BASES as f64; + let three_mean = three_prime_sum / NUM_PRIME_BASES as f64; + let whole_mean = whole_sum / len as f64; + + // Qualimap pushes bias values for all qualifying transcripts unconditionally + // (lines 247-249 of TranscriptDataHandler.java). Since pickTranscripts() + // already ensures mean >= 1.0, whole_mean is always positive. The 5'-3' + // ratio may produce infinity or NaN when three_mean == 0; Java's + // StatUtils.percentile handles these via Arrays.sort which places NaN + // at the end. We filter NaN values since they don't contribute meaningful + // information to the median. + five_prime_biases.push(five_mean / whole_mean); + three_prime_biases.push(three_mean / whole_mean); + let ratio = five_mean / three_mean; + if !ratio.is_nan() { + five_three_biases.push(ratio); + } + } + + let five = median(&mut five_prime_biases); + let three = median(&mut three_prime_biases); + let five_three = median(&mut five_three_biases); + + (five, three, five_three) +} + +/// Compute the median of a slice of f64 values. +fn median(values: &mut [f64]) -> f64 { + if values.is_empty() { + return f64::NAN; + } + values.sort_by(|a, b| a.partial_cmp(b).unwrap_or(std::cmp::Ordering::Equal)); + let n = values.len(); + if n.is_multiple_of(2) { + (values[n / 2 - 1] + values[n / 2]) / 2.0 + } else { + values[n / 2] + } +} + +// ============================= Output Writers ================================== + +/// Write the coverage profile TSV file. +/// +/// Format: tab-separated, header line starting with `#`, 100 rows (0.0–99.0). +fn write_coverage_profile(profile: &[f64; NUM_BINS], path: &Path) -> Result<()> { + use std::fs::File; + + let mut f = File::create(path) + .with_context(|| format!("Failed to create coverage profile: {}", path.display()))?; + + writeln!(f, "#Transcript position\tTranscript coverage profile")?; + + for (i, &val) in profile.iter().enumerate() { + writeln!(f, "{:.1}\t{}", i as f64, val)?; + } + + Ok(()) +} + +/// Write the complete Qualimap RNA-Seq QC results file. +/// +/// Produces `rnaseq_qc_results.txt` in exact Qualimap format with all sections: +/// Input, Reads alignment, Reads genomic origin, Transcript coverage profile, +/// and Junction analysis. +#[allow(clippy::too_many_arguments)] +pub fn write_qualimap_results( + result: &QualimapResult, + index: &QualimapIndex, + bam_path: &str, + gtf_path: &str, + stranded: u8, + output_dir: &Path, +) -> Result<()> { + // Auto-detect paired mode from the data + let paired = result.left_proper_in_pair > 0 || result.right_proper_in_pair > 0; + use std::fs; + + fs::create_dir_all(output_dir) + .with_context(|| format!("Failed to create output dir: {}", output_dir.display()))?; + + // --- Build per-transcript coverage entries --- + let entries = build_transcript_entries(&result.transcript_coverage_raw, index); + + // --- Compute coverage profiles --- + // Qualimap uses ALL transcripts with coverage > 0, sorted by mean coverage. + // The profile is a SUM of per-transcript length-normalized histograms. + let active_entries: Vec<&TranscriptCoverageEntry> = + entries.iter().filter(|e| e.mean_coverage > 0.0).collect(); + let total_profile = compute_coverage_profile(&active_entries); + + log::debug!( + "QM_PROFILE: {} total entries, {} active (mean>0)", + entries.len(), + active_entries.len() + ); + + // Sort by mean coverage for high/low tiers + let mut sorted_by_mean: Vec<&TranscriptCoverageEntry> = active_entries.clone(); + sorted_by_mean.sort_by(|a, b| { + a.mean_coverage + .partial_cmp(&b.mean_coverage) + .unwrap_or(std::cmp::Ordering::Equal) + }); + + // Low: bottom N transcripts (ascending order) + let low_entries: Vec<&TranscriptCoverageEntry> = sorted_by_mean + .iter() + .take(LOW_TIER_COUNT) + .copied() + .collect(); + let low_profile = compute_coverage_profile(&low_entries); + + // High: top N transcripts (descending order) + let high_entries: Vec<&TranscriptCoverageEntry> = sorted_by_mean + .iter() + .rev() + .take(HIGH_TIER_COUNT) + .copied() + .collect(); + let high_profile = compute_coverage_profile(&high_entries); + + // --- Compute bias --- + let (five_bias, three_bias, five_three_bias) = compute_bias(&entries); + + // --- Write coverage profile TSVs --- + let raw_data_dir = output_dir.join("raw_data_qualimapReport"); + fs::create_dir_all(&raw_data_dir)?; + + write_coverage_profile( + &total_profile, + &raw_data_dir.join("coverage_profile_along_genes_(total).txt"), + )?; + write_coverage_profile( + &high_profile, + &raw_data_dir.join("coverage_profile_along_genes_(high).txt"), + )?; + write_coverage_profile( + &low_profile, + &raw_data_dir.join("coverage_profile_along_genes_(low).txt"), + )?; + + info!("Wrote coverage profiles to {}", raw_data_dir.display()); + + // --- Write rnaseq_qc_results.txt --- + let results_path = output_dir.join("rnaseq_qc_results.txt"); + write_results_file( + result, + bam_path, + gtf_path, + paired, + stranded, + five_bias, + three_bias, + five_three_bias, + &results_path, + )?; + + info!("Wrote {}", results_path.display()); + + Ok(()) +} + +/// Write the rnaseq_qc_results.txt file in exact Qualimap format. +#[allow(clippy::too_many_arguments)] +fn write_results_file( + result: &QualimapResult, + bam_path: &str, + gtf_path: &str, + paired: bool, + stranded: u8, + five_bias: f64, + three_bias: f64, + five_three_bias: f64, + path: &Path, +) -> Result<()> { + use std::fs::File; + + let mut f = + File::create(path).with_context(|| format!("Failed to create {}", path.display()))?; + + // Header + writeln!(f, "RNA-Seq QC report")?; + writeln!(f, "-----------------------------------")?; + writeln!(f)?; + + // >>>>>>> Input + writeln!(f, ">>>>>>> Input")?; + writeln!(f)?; + writeln!(f, " bam file = {bam_path}")?; + writeln!(f, " gff file = {gtf_path}")?; + writeln!(f, " counting algorithm = uniquely-mapped-reads")?; + let protocol = match stranded { + 1 => "strand-specific-forward", + 2 => "strand-specific-reverse", + _ => "non-strand-specific", + }; + writeln!(f, " protocol = {protocol}")?; + writeln!(f, " 5'-3' bias region size = {NUM_PRIME_BASES}")?; + writeln!( + f, + " 5'-3' bias number of top transcripts = {NUM_TRANSCRIPTS_FOR_BIAS}" + )?; + writeln!(f)?; + writeln!(f)?; + + // >>>>>>> Reads alignment + writeln!(f, ">>>>>>> Reads alignment")?; + writeln!(f)?; + + if paired { + writeln!( + f, + " reads aligned (left/right) = {} / {}", + format_with_commas(result.left_proper_in_pair), + format_with_commas(result.right_proper_in_pair) + )?; + writeln!( + f, + " read pairs aligned = {}", + format_with_commas(result.both_proper_in_pair / 2) + )?; + } else { + writeln!( + f, + " reads aligned = {}", + format_with_commas(result.read_count) + )?; + } + writeln!( + f, + " total alignments = {}", + format_with_commas(result.primary_alignments + result.secondary_alignments) + )?; + writeln!( + f, + " secondary alignments = {}", + format_with_commas(result.secondary_alignments) + )?; + writeln!( + f, + " non-unique alignments = {}", + format_with_commas(result.alignment_not_unique) + )?; + writeln!( + f, + " aligned to genes = {}", + format_with_commas(result.exonic_reads) + )?; + writeln!( + f, + " ambiguous alignments = {}", + format_with_commas(result.ambiguous_reads) + )?; + writeln!( + f, + " no feature assigned = {}", + format_with_commas(result.no_feature) + )?; + writeln!( + f, + " not aligned = {}", + format_with_commas(result.not_aligned) + )?; + + // SSP estimation — only written when protocol was not pre-specified (stranded == 0) + // When the user specifies --stranded, Qualimap does not output this line. + if stranded == 0 { + let ssp_total = result.ssp_fwd + result.ssp_rev; + if ssp_total > 0 { + let fwd = result.ssp_fwd as f64 / ssp_total as f64; + let rev = result.ssp_rev as f64 / ssp_total as f64; + writeln!(f, " SSP estimation (fwd/rev) = {:.2} / {:.2}", fwd, rev)?; + } + } + writeln!(f)?; + writeln!(f)?; + + // >>>>>>> Reads genomic origin + writeln!(f, ">>>>>>> Reads genomic origin")?; + writeln!(f)?; + + let total_classified = result.exonic_reads + result.intronic_reads + result.intergenic_reads; + if total_classified > 0 { + let exonic_pct = result.exonic_reads as f64 / total_classified as f64 * 100.0; + let intronic_pct = result.intronic_reads as f64 / total_classified as f64 * 100.0; + let intergenic_pct = result.intergenic_reads as f64 / total_classified as f64 * 100.0; + + // overlapping exon percentage is relative to total classified + let overlapping_pct = + result.overlapping_exon_reads as f64 / total_classified as f64 * 100.0; + + writeln!( + f, + " exonic = {} ({}%)", + format_with_commas(result.exonic_reads), + format_percentage(exonic_pct) + )?; + writeln!( + f, + " intronic = {} ({}%)", + format_with_commas(result.intronic_reads), + format_percentage(intronic_pct) + )?; + writeln!( + f, + " intergenic = {} ({}%)", + format_with_commas(result.intergenic_reads), + format_percentage(intergenic_pct) + )?; + writeln!( + f, + " overlapping exon = {} ({}%)", + format_with_commas(result.overlapping_exon_reads), + format_percentage(overlapping_pct) + )?; + } + writeln!(f)?; + writeln!(f)?; + + // >>>>>>> Transcript coverage profile + writeln!(f, ">>>>>>> Transcript coverage profile")?; + writeln!(f)?; + writeln!(f, " 5' bias = {}", format_bias(five_bias))?; + writeln!(f, " 3' bias = {}", format_bias(three_bias))?; + writeln!(f, " 5'-3' bias = {}", format_bias(five_three_bias))?; + writeln!(f)?; + writeln!(f)?; + + // >>>>>>> Junction analysis + writeln!(f, ">>>>>>> Junction analysis")?; + writeln!(f)?; + writeln!( + f, + " reads at junctions = {}", + format_with_commas(result.reads_at_junctions) + )?; + writeln!(f)?; + + // Sort junction motifs by percentage descending + if result.reads_at_junctions > 0 { + let total_junctions = result.reads_at_junctions as f64; + let mut motif_pcts: Vec<(String, f64)> = result + .junction_motifs + .iter() + .map(|(motif, &count)| (motif.clone(), count as f64 * 100.0 / total_junctions)) + .collect(); + motif_pcts.sort_by(|a, b| b.1.partial_cmp(&a.1).unwrap_or(std::cmp::Ordering::Equal)); + + // Qualimap shows top 11 motifs (count <= 10 in their loop) + for (motif, pct) in motif_pcts.iter().take(11) { + writeln!(f, " {} : {:.2}%", motif, pct)?; + } + } + writeln!(f)?; + + Ok(()) +} + +/// Build transcript coverage entries from the raw per-transcript coverage. +/// +/// Uses the raw `TranscriptCoverage` (keyed by flat transcript index) to avoid +/// the overhead and potential collisions of string-keyed lookup. +fn build_transcript_entries( + coverage: &TranscriptCoverage, + index: &QualimapIndex, +) -> Vec { + let mut entries = Vec::new(); + + for (flat_idx, tx_info) in index.transcripts.iter().enumerate() { + let flat_idx = flat_idx as u32; + match coverage.get(flat_idx) { + Some(depth) => { + let sum: f64 = depth.iter().map(|&v| v as f64).sum(); + let mean = if depth.is_empty() { + 0.0 + } else { + sum / depth.len() as f64 + }; + entries.push(TranscriptCoverageEntry { + coverage: depth.to_vec(), + mean_coverage: mean, + strand: tx_info.strand, + gene_idx: tx_info.gene_idx, + flat_idx, + }); + } + None => { + // Transcript with no coverage — still include for total count + entries.push(TranscriptCoverageEntry { + coverage: vec![0; tx_info.exonic_length as usize], + mean_coverage: 0.0, + strand: tx_info.strand, + gene_idx: tx_info.gene_idx, + flat_idx, + }); + } + } + } + + entries +} + +// ============================= Tests =========================================== + +#[cfg(test)] +mod tests { + use super::*; + + #[test] + fn test_format_with_commas() { + assert_eq!(format_with_commas(0), "0"); + assert_eq!(format_with_commas(999), "999"); + assert_eq!(format_with_commas(1000), "1,000"); + assert_eq!(format_with_commas(1234567), "1,234,567"); + assert_eq!(format_with_commas(87559392), "87,559,392"); + } + + #[test] + fn test_format_percentage() { + assert_eq!(format_percentage(68.30), "68.3"); + assert_eq!(format_percentage(29.69), "29.69"); + assert_eq!(format_percentage(2.01), "2.01"); + assert_eq!(format_percentage(9.31), "9.31"); + assert_eq!(format_percentage(100.00), "100.0"); + } + + #[test] + fn test_format_bias() { + assert_eq!(format_bias(0.71), "0.71"); + assert_eq!(format_bias(0.57), "0.57"); + assert_eq!(format_bias(1.30), "1.3"); + assert_eq!(format_bias(1.47), "1.47"); + assert_eq!(format_bias(0.22), "0.22"); + } + + #[test] + fn test_median() { + assert_eq!(median(&mut vec![1.0, 3.0, 2.0]), 2.0); + assert_eq!(median(&mut vec![1.0, 2.0, 3.0, 4.0]), 2.5); + assert!(median(&mut vec![]).is_nan()); + } + + /// Helper: build a single-transcript slice for compute_coverage_profile. + fn single_entry(coverage: Vec) -> TranscriptCoverageEntry { + let mean = if coverage.is_empty() { + 0.0 + } else { + coverage.iter().map(|&v| v as f64).sum::() / coverage.len() as f64 + }; + TranscriptCoverageEntry { + coverage, + mean_coverage: mean, + strand: '+', + gene_idx: 0, + flat_idx: 0, + } + } + + // ---- compute_coverage_profile tests matching Qualimap's GenericHistogram ---- + + /// Uniform array of length 100: step=1, each bin = 1.0/100 = 0.01. + #[test] + fn test_coverage_profile_binning_uniform_100() { + let entry = single_entry(vec![1; 100]); + let profile = compute_coverage_profile(&[&entry]); + for (i, &val) in profile.iter().enumerate() { + assert!( + (val - 0.01).abs() < 1e-10, + "bin {i}: expected 0.01, got {val}" + ); + } + } + + /// Uniform array of length 200: step=2, each bin = 2.0/200 = 0.01. + #[test] + fn test_coverage_profile_binning_uniform_200() { + let entry = single_entry(vec![1; 200]); + let profile = compute_coverage_profile(&[&entry]); + for (i, &val) in profile.iter().enumerate() { + assert!( + (val - 0.01).abs() < 1e-10, + "bin {i}: expected 0.01, got {val}" + ); + } + } + + /// Uniform array of length 150: step=2, 75 bins filled (each ≈ 0.01333), bins 75-99 = 0.0. + #[test] + fn test_coverage_profile_binning_uniform_150() { + let entry = single_entry(vec![1; 150]); + let profile = compute_coverage_profile(&[&entry]); + let expected_filled = 2.0 / 150.0; // 0.01333... + for (i, &val) in profile.iter().enumerate() { + if i < 75 { + assert!( + (val - expected_filled).abs() < 1e-10, + "bin {i}: expected {expected_filled}, got {val}" + ); + } else { + assert!( + val.abs() < 1e-10, + "bin {i}: expected 0.0 (unfilled), got {val}" + ); + } + } + } + + /// Ramp array [0, 1, ..., 99], length 100: step=1, bin i = i/100.0. + #[test] + fn test_coverage_profile_binning_ramp_100() { + let coverage: Vec = (0..100).collect(); + let entry = single_entry(coverage); + let profile = compute_coverage_profile(&[&entry]); + for (i, &val) in profile.iter().enumerate() { + let expected = i as f64 / 100.0; + assert!( + (val - expected).abs() < 1e-10, + "bin {i}: expected {expected}, got {val}" + ); + } + } + + /// Short uniform array of length 50: step=1 (clamped), 50 bins filled (each = 1.0/50 = 0.02), + /// bins 50-99 = 0.0. + #[test] + fn test_coverage_profile_binning_short_50() { + let entry = single_entry(vec![1; 50]); + let profile = compute_coverage_profile(&[&entry]); + let expected_filled = 1.0 / 50.0; // 0.02 + for (i, &val) in profile.iter().enumerate() { + if i < 50 { + assert!( + (val - expected_filled).abs() < 1e-10, + "bin {i}: expected {expected_filled}, got {val}" + ); + } else { + assert!( + val.abs() < 1e-10, + "bin {i}: expected 0.0 (unfilled), got {val}" + ); + } + } + } + + #[test] + fn test_coverage_profile_single_transcript() { + // Simple transcript: 200 bases, uniform coverage of 10 + let entry = TranscriptCoverageEntry { + coverage: vec![10; 200], + mean_coverage: 10.0, + strand: '+', + gene_idx: 0, + flat_idx: 0, + }; + let entries: Vec<&TranscriptCoverageEntry> = vec![&entry]; + let profile = compute_coverage_profile(&entries); + + // Each bin should have roughly 10.0 (normalized by length) + // With 200 bases and 100 bins: step=2, each bin sums 2 values of 10 = 20 + // Divided by norm (200) = 0.1 per bin? No... + // Actually: bin_coverage = sum of values in bin = 20 + // hist[bin] += bin_coverage / norm = 20 / 200 = 0.1 + for &val in profile.iter() { + assert!((val - 0.1).abs() < 1e-10, "Expected 0.1, got {val}"); + } + } +} diff --git a/tests/integration_test.rs b/tests/integration_test.rs index 43b31ee..47cc1de 100644 --- a/tests/integration_test.rs +++ b/tests/integration_test.rs @@ -573,8 +573,8 @@ fn test_multiple_bam_files() { /// Passing the same BAM file twice should fail with a duplicate-stem error. #[test] fn test_duplicate_bam_stems_rejected() { - let bin = env!("CARGO_BIN_EXE_rustqc"); - let output = Command::new(bin) + let bin = rustqc_binary(); + let output = Command::new(&bin) .args([ "rna", "tests/data/test.bam",