From: Heng Li <lh3@live.co.uk>
Date: Tue, 16 Nov 2010 19:11:58 +0000 (+0000)
Subject: remove ZQ if both BQ and ZQ are present
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=796a36ed12f01950213be16533e79ab0508744f4;p=samtools.git

remove ZQ if both BQ and ZQ are present
---

diff --git a/bam_md.c b/bam_md.c
index e1e756d..44d46a4 100644
--- a/bam_md.c
+++ b/bam_md.c
@@ -173,7 +173,10 @@ int bam_prob_realn_core(bam1_t *b, const char *ref, int apply_baq)
 	// test if BQ or ZQ is present
 	if ((bq = bam_aux_get(b, "BQ")) != 0) ++bq;
 	if ((zq = bam_aux_get(b, "ZQ")) != 0 && *zq == 'Z') ++zq;
-	if (bq && zq) return -2; // do not know what to do...
+	if (bq && zq) { // remove the ZQ tag
+		bam_aux_del(b, zq-1);
+		zq = 0;
+	}
 	if (bq || zq) {
 		if ((apply_baq && zq) || (!apply_baq && bq)) return -3; // in both cases, do nothing
 		if (bq && apply_baq) { // then convert BQ to ZQ