From: Derek Barnett <derekwbarnett@gmail.com>
Date: Mon, 10 Dec 2012 16:59:56 +0000 (-0500)
Subject: Fixed: BamWriter - quality string starting with '*' (GH issue #68)
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;ds=sidebyside;h=2fe0265511837d14f354a7f4f7cfaf42ceb07826;hp=f7d86e0fa7161081f69c5c178ee0141bea599f71;p=bamtools.git

Fixed: BamWriter - quality string starting with '*' (GH issue #68)
---

diff --git a/src/api/internal/bam/BamWriter_p.cpp b/src/api/internal/bam/BamWriter_p.cpp
index 1bb086f..637bb7a 100644
--- a/src/api/internal/bam/BamWriter_p.cpp
+++ b/src/api/internal/bam/BamWriter_p.cpp
@@ -284,7 +284,7 @@ void BamWriterPrivate::WriteAlignment(const BamAlignment& al) {
 
         // write the base qualities
         char* pBaseQualities = new char[queryLength]();
-        if ( al.Qualities.empty() || al.Qualities[0] == '*' || al.Qualities[0] == (char)0xFF )
+        if ( al.Qualities.empty() || ( al.Qualities.size() == 1 && al.Qualities[0] == '*' ) || al.Qualities[0] == (char)0xFF )
             memset(pBaseQualities, 0xFF, queryLength); // if missing or '*', fill with invalid qual
         else {
             for ( size_t i = 0; i < queryLength; ++i )