Fixed: BamWriter behavior on missing quality string (0xFF)

 * See Issue #65

diff --git a/src/api/internal/bam/BamWriter_p.cpp b/src/api/internal/bam/BamWriter_p.cpp
index 887780063b70d2ce29bf6c0ea0182a5c5a90724b..1bb086f4725c78ed75b7acb3ac3c8387948461f4 100644 (file)
--- a/src/api/internal/bam/BamWriter_p.cpp
+++ b/src/api/internal/bam/BamWriter_p.cpp
@@ -2,7 +2,7 @@
 // BamWriter_p.cpp (c) 2010 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
 // ---------------------------------------------------------------------------
-// Last modified: 4 April 2012 (DB)
+// Last modified: 18 November 2012 (DB)
 // ---------------------------------------------------------------------------
 // Provides the basic functionality for producing BAM files
 // ***************************************************************************
@@ -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 == "*" )
+        if ( al.Qualities.empty() || 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 )