count secondary alignments

sjaenick · Apr 20, 2023 · 2b8d9b8 · 2b8d9b8
1 parent fdf287e
commit 2b8d9b8
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/bamstats.c b/bamstats.c
@@ -48,7 +48,7 @@ int bam_reader(char* bamfile, char* outfile) {
     uint64_t cnt;
     bam1_t *b = bam_init1();
     while (bam_read1(fp, b) >= 0) {
-        if (((b->core.flag & 0x4) == 0) && ((b->core.flag & 0x100) == 0) && ((b->core.flag & 0x400) == 0)) {
+        if (((b->core.flag & 0x4) == 0) && ((b->core.flag & 0x400) == 0)) {
             int32_t tid = b->core.tid;
             char* ref = hdr->target_name[tid];
             k = kh_get(str, h, ref);