Remove dead genebody coverage code

AGENTS.md

@@ -68,7 +68,6 @@ src/
     featurecounts/
       mod.rs        — Re-exports output
       output.rs     — featureCounts-format output & biotype counting
-    genebody.rs     — Gene body coverage profiling, Qualimap-compatible output
     preseq.rs       — preseq lc_extrap library complexity extrapolation
     rseqc/
       mod.rs                — Re-exports all RSeQC modules + common helpers
@@ -262,18 +261,14 @@ forwarded to `count_reads()` as the `skip_dup_check: bool` parameter).
   `infer_experiment:`, `read_duplication:`, `read_distribution:`, `junction_annotation:`,
   `junction_saturation:`, `inner_distance:`). Each has an `enabled: bool` toggle
   and tool-specific parameter overrides. CLI flags take precedence over config values.
-- The YAML config also has sections for `tin:`, `preseq:`, `genebody_coverage:`,
+- The YAML config also has sections for `tin:`, `preseq:`,
   `flagstat:`, `idxstats:`, and `samtools_stats:`. Each has an `enabled: bool` toggle.
   Preseq has additional parameters: `max_extrap`, `step_size`, `n_bootstraps`,
   `confidence_level`, `seed`, `max_terms`, `defects`. TIN has `sample_size` and
   `min_coverage`.
 - The `featurecounts.rs` module produces featureCounts-compatible output files (counts TSV,
   summary, biotype counts, and MultiQC files). These are generated in the same pass as
   the dupRadar analysis — no separate featureCounts run is needed.
-- The genebody module (`genebody.rs`) produces Qualimap-compatible output files
-  (`coverage_profile_along_genes_(total).txt` and `rnaseq_qc_results.txt`). These
-  files are written to a `qualimap/` subdirectory and are parseable by MultiQC as
-  Qualimap rnaseq reports. Gene body coverage only runs in GTF mode.
 - The GTF parser (`gtf.rs`) accepts extra attribute names to extract (e.g., `gene_biotype`,
   `gene_type`) and stores them in `Gene.attributes`. The biotype attribute name is
   configurable via `--biotype-attribute` CLI flag or `featurecounts.biotype_attribute`

CONTRIBUTING.md

@@ -74,7 +74,6 @@ src/
     featurecounts/
       mod.rs                     Re-exports output
       output.rs                  featureCounts-format output and biotype counting
-    genebody.rs                Gene body coverage profiling, Qualimap-compatible output
     preseq.rs                  preseq lc_extrap library complexity extrapolation
     rseqc/
       mod.rs                     Re-exports all RSeQC modules + common helpers

docs/src/content/docs/usage/configuration.md

@@ -83,10 +83,6 @@ tin:
   sample_size: 100
   min_coverage: 10
 
-# Gene body coverage / Qualimap
-genebody_coverage:
-  enabled: true
-
 # Library complexity (preseq lc_extrap)
 preseq:
   enabled: true
@@ -314,17 +310,6 @@ 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    # Legacy toggle for the older gene body coverage module
-```
-
-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
 
 ```yaml

src/config.rs

@@ -101,10 +101,6 @@ pub struct Config {
     #[serde(default)]
     pub tin: TinConfig,
 
-    /// Gene body coverage + Qualimap-compatible output configuration.
-    #[serde(default)]
-    pub genebody_coverage: GenebodyCoverageConfig,
-
     /// samtools stats-compatible output configuration (SN section).
     #[serde(default)]
     pub samtools_stats: SamtoolsStatsConfig,
@@ -516,23 +512,6 @@ impl Default for TinConfig {
     }
 }
 
-/// Configuration for gene body coverage and Qualimap-compatible output.
-///
-/// When enabled, produces a coverage profile along gene bodies and a
-/// Qualimap-compatible `rnaseq_qc_results.txt` file parseable by MultiQC.
-#[derive(Debug, Deserialize)]
-#[serde(default)]
-pub struct GenebodyCoverageConfig {
-    /// Whether to produce gene body coverage output. Defaults to true.
-    pub enabled: bool,
-}
-
-impl Default for GenebodyCoverageConfig {
-    fn default() -> Self {
-        Self { enabled: true }
-    }
-}
-
 /// Configuration for Qualimap RNA-Seq QC.
 ///
 /// When enabled, produces Qualimap-compatible output files including

src/main.rs

@@ -645,13 +645,6 @@ fn process_single_bam(
         || rseqc_config.inner_distance_enabled
         || rseqc_config.preseq_enabled;
 
-    // === Build gene body coverage position map (if enabled) ===
-    let genebody_position_map = if params.config.genebody_coverage.enabled {
-        genes.map(rna::genebody::TranscriptPositionMap::from_genes)
-    } else {
-        None
-    };
-
     // === Build Qualimap exon index (if enabled, GTF-only) ===
     let qualimap_index = if params.config.qualimap.enabled {
         genes.map(rna::qualimap::QualimapIndex::from_genes)
@@ -686,7 +679,6 @@ fn process_single_bam(
             } else {
                 None
             },
-            genebody_position_map.as_ref(),
             qualimap_index.as_ref(),
         )?;
         info!(