From 4c7dded669ca354c32b6639ee91cc6f88c32df1f Mon Sep 17 00:00:00 2001
From: David Jones <you@example.com>
Date: Mon, 13 Nov 2017 16:06:59 +0000
Subject: [PATCH] Fixes #64

---
 src/bam_access.c | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/src/bam_access.c b/src/bam_access.c
index b37eaec..3ebab6d 100644
--- a/src/bam_access.c
+++ b/src/bam_access.c
@@ -102,6 +102,11 @@ 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;
   }