// 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
// ***************************************************************************
// write the base qualities
char* pBaseQualities = new char[queryLength]();
- if ( al.Qualities.empty() || al.Qualities == "*" )
+ 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 )