remove uneeded

Author: brentp

README.md

@@ -1,7 +1,6 @@
 # bpbio: a single binary with a collection of sub-commands useful for genomics
 
 + plot-sv-vcf: create a plot that shows the number of large and small variants separated by DEL/DUP/BND/INV for a multi-sample SV VCF. (idea from @ernfrid)
-+ variexpr: simple expression on variants for great good
 
 
 ## Libraries
@@ -15,39 +14,3 @@
 
 + homsv: look for depth changes in self-chains or homologous regions
 + homsv-merge: merge output from homsv
-
-## Variexpr
-
-variexpr finds all trios in a VCF, PED pair and let's the user specify an expression with indentifiers
-of `kid`, `mom`, `dad` that is applied to each possible trio. samples that pass that filter have the id
-of the kid added to the INFO field.
-
-```
-bpbio variexpr \
-   --pass-only \ # output only variants that pass one of the filters.
-   --vcf $vcf \
-   --ped $ped \
-   --load functions.js \ 
-   --out-vcf annotated.bcf \
-   --info "variant.call_rate > 0.9" \ # this filter is applied before the trio filters and can speed evaluation if it is stringent.
-   --trio "denovo:kid.alts == 1 && mom.alts == 0 && dad.alts == 0 \
-                   && kid.AB > 0.25 && kid.AB < 0.75 \
-                   && (mom.AD[1] + dad.AD[1]) == 0 \
-                   && kid.GQ >= 20 && mom.GQ >= 20 && dad.GQ >= 20 \
-                   && kid.DP >= 12 && mom.DP >= 12 && dad.DP >= 12" \
-   --trio "informative:kid.GQ > 20 && dad.GQ > 20 && mom.GQ > 20 && kid.alts == 1 && ((mom.alts == 1 && dad.alts == 0) || (mom.alts == 0 && dad.alts == 1))" \
-   --trio "recessive:recessive_func(kid, mom, dad)"
-
-
-Note that `variexpr` does not give direct access to the genotypes, instead exposing `alts` where 0 is homozygous reference, 1 is heterozygous, 2 is
-homozygous alternate and -1 when the genotype is unknown. It is recommended to **decompose** a VCF before sending to `variexpr`
-
-### Attributes
-
- + anything in the INFO is available as e.g. INFO.CSQ
- + if FORMAT.AB is not present, it is added so one can filter with kid.AB > 0.25 && kid.AB < 0.25
- + variant attributes are: `CHROM`, `POS`, `start`, `end`, `ID`, `REF`, `ALT`, `QUAL`, `FILTER`
- + calculated variant attributes include: `aaf`, `hwe_score`, `call_rate`, `num_hom_ref`, `num_het`, `num_hom_alt`, `num_unknown`
-
- + sample attributes (via `kid`, `mom`, `dad`) include in the FORMAT. available as e.g. kid.AD[1]
- + sample attributes from the ped for `affected`, `sex` are available as, e.g. kid.sex.

src/bpbio.nim

@@ -5,7 +5,7 @@ import bpbiopkg/plotsvvcf
 from bpbiopkg/info import version
 #import bpbiopkg/fastcov
 #import bpbiopkg/homsv
-import bpbiopkg/variexpr
+#import bpbiopkg/variexpr
 #export fastcov
 import strformat
 import tables
@@ -17,7 +17,7 @@ type pair = object
 
 var dispatcher = {
   "plot-sv-vcf": pair(f:plotsvvcf.main, description:"make a plot of SV types across samples for a multi-sample SV VCF"),
-  "variexpr": pair(f:variexpr.main, description:"simple expression to filter or annotate VCFs"),
+  #"variexpr": pair(f:variexpr.main, description:"simple expression to filter or annotate VCFs"),
   #"homsv": pair(f:homsv.main, description:"look for depth changes in self-chains or homologous regions"),
   #"homsv-merge": pair(f:homsv.merge, description:"merge output from homsv"),
   }.toTable