Merge pull request #72 from cancerit/feature/avg_rd_len_sec_supp_rds

Fixes #64
cancerit · Mar 6, 2018 · b012f94 · b012f94
2 parents 9194008 + 4c7dded
commit b012f94
Showing 1 changed file with 5 additions and 0 deletions.
diff --git a/src/bam_access.c b/src/bam_access.c
@@ -105,6 +105,11 @@ int bam_access_get_avg_readlength_from_bam(htsFile *sf){
   bam1_t *b = bam_init1();
   int ret;
   while ((ret = sam_read1(sf, head, b)) >= 0 && read_count < 100) {
+		if((b->core.flag & BAM_FSECONDARY)
+		|| (b->core.flag & BAM_FSUPPLEMENTARY)
+		|| (b->core.flag & BAM_FQCFAIL)){
+			continue;
+		}
     read_count++;
     read_length_sum += b->core.l_qseq;
   }