fix long-standing bug (#27) that would cause sigsegv in some cases

Author: brentp

CHANGES.md

@@ -1,3 +1,7 @@
+v0.2.4
+======
++ fix long-standing bug (#27) that would cause sigsegv in some cases
+
 v0.2.3
 ======
 + add `feature_fusion` to impact order list (#92)

js/slivar-functions.js

@@ -5,7 +5,7 @@ function hq(kid, mom, dad) {
 }
 
 function hq1(sample) {
-  if (sample.unknown || sample.GQ < config.min_GQ) { return false; }
+  if (sample.unknown || (sample.GQ < config.min_GQ)) { return false; }
   if ((sample.AD[0] + sample.AD[1]) < config.min_DP) { return false; }
   if (sample.hom_ref){
       return sample.AB < 0.02
@@ -16,11 +16,6 @@ function hq1(sample) {
   return sample.AB > 0.98
 }
 
-function hqrv(variant, INFO, af_cutoff) {
-  // hi-quality, rare variant.
-  return INFO.gnomad_popmax_af < af_cutoff && variant.FILTER == 'PASS'
-}
-
 function denovo(kid, mom, dad){
   // check genotypes match expected pattern
   if(!(kid.het && mom.hom_ref && dad.hom_ref)){ return false; }

src/slivarpkg/evaluator.nim

@@ -438,9 +438,11 @@ proc id2names*(h:Header): seq[idpair] =
   ## lookup of headerid -> name
   var hdr = h.hdr
   result = newSeq[idpair](hdr.n[0])
-  for i in 0..<hdr.n[0].int:
-    var idp = cast[seq[bcf_idpair_t]](hdr.id[0])[i]
-    if idp.val == nil or idp.key.len == 0: continue
+  let arr = cast[ptr UncheckedArray[bcf_idpair_t]](hdr.id[0])
+  for i in 0..<hdr.n[0].int32:
+    var idp = arr[i]
+    if idp.val == nil or idp.key == nil: continue
+    if idp.key.len == 0: continue
     var name = idp.key
     if idp.val.hrec[1] == nil and idp.val.hrec[2] == nil: continue
     if idp.val.id >= result.len:
@@ -795,7 +797,10 @@ proc set_format_fields*(ev:var Evaluator, v:Variant, alts: var seq[int8], ints:
         stderr.write_line &"""         expected 2 values per sample for 'AD' field, but got {ints.len / ev.samples.len:.1f} for variant: {v.CHROM}:{v.start + 1}:{v.REF}:{join(v.ALT, ",")}"""
         stderr.write_line """         see: https://github.com/brentp/slivar/wiki/decomposing-and-subsetting-vcfs"""
       if not has_ab:
-        ev.set_ab(fmt, ints, v.ALT.len + 1)
+        if ev.samples.len * (1 + valt_len) == ints.len:
+          ev.set_ab(fmt, ints, v.ALT.len + 1)
+        else:
+          ev.fmt_field_sets.curr.excl(f.i.uint8)
         has_ab = true
 
     elif f.name == "AB":

src/slivarpkg/version.nim

@@ -1,2 +1,2 @@
-const slivarVersion* = "0.2.3"
+const slivarVersion* = "0.2.4"
 const slivarGitCommit* = staticExec("git rev-parse --verify HEAD")

tests/functional-tests.sh

@@ -196,4 +196,5 @@ assert_in_stderr "sample	compound-het
 SID_3	2
 SID_4	2"
 
+run check_issue_27 $exe expr -g _clinvar.test.zip -v tests/test-27.vcf.gz