update to new hts-nim mapping_quality

closes #4
brentp · Aug 1, 2018 · e4249bf · e4249bf
1 parent 3d390f1
commit e4249bf
Show file tree

Hide file tree

Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/src/bam_filter.nim b/src/bam_filter.nim
@@ -68,7 +68,7 @@ example:
 
   for aln in bam:
     ex.clear()
-    discard ke_set_int(ex.ke, "mapq", aln.qual.cint)
+    discard ke_set_int(ex.ke, "mapq", aln.mapping_quality.cint)
     discard ke_set_int(ex.ke, "start", aln.start.cint)
     discard ke_set_int(ex.ke, "pos", (aln.start + 1).cint)
     discard ke_set_int(ex.ke, "flag", (aln.flag).cint)

diff --git a/src/count_reads.nim b/src/count_reads.nim
@@ -71,7 +71,7 @@ proc internal_count(bam:Bam, mapq:uint8, eflag:uint16, regions:TableRef[string,
       continue
     var lap:Lapper[region_t] = lapify(regions[chrom])
     for aln in bam.querys(chrom):
-      if aln.qual < mapq: continue
+      if aln.mapping_quality < mapq: continue
       if (aln.flag and eflag) != 0: continue
 
       lap.each_seek(aln.start, aln.stop, inc_count)