From: Heng Li <lh3@live.co.uk>
Date: Thu, 18 Nov 2010 02:47:20 +0000 (+0000)
Subject: minor change to how seqQ is applied
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=3d0fb2fa78f3cafc854fde0a9b5ea56047f2890a;p=samtools.git

minor change to how seqQ is applied
---

diff --git a/bam2bcf_indel.c b/bam2bcf_indel.c
index 8b80e3f..790f59e 100644
--- a/bam2bcf_indel.c
+++ b/bam2bcf_indel.c
@@ -625,6 +625,7 @@ int bcf_call_mnp_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
 				seqQ = _seqQ[K];
 				tmp = sc[0]>>6 & 0xff;
 				indelQ = tmp > 111? 0 : (int)((1. - tmp/111.) * indelQ + .499); // reduce indelQ
+				if (indelQ > seqQ) indelQ = seqQ; // this is different from indel calling!
 				p->aux = (sc[0]&0x3f)<<16 | seqQ<<8 | indelQ;
 				sumq[sc[0]&0x3f] += indelQ < seqQ? indelQ : seqQ;
 			}
diff --git a/bamtk.c b/bamtk.c
index 6d7b832..591257b 100644
--- a/bamtk.c
+++ b/bamtk.c
@@ -9,7 +9,7 @@
 #endif
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.10-1 (r831)"
+#define PACKAGE_VERSION "0.1.10-2 (r832)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);