From: Erik Garrison <erik.garrison@bc.edu>
Date: Fri, 7 Dec 2012 23:07:55 +0000 (-0500)
Subject: resolve bamtools #68
X-Git-Url: https://git.donarmstrong.com/?p=bamtools.git;a=commitdiff_plain;h=33add6354f2be9b268450de9002644bd220acf6b

resolve bamtools #68

Check that the quality string is fully comprised of "*", rather than if
the first character is "*".
---

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 )