// BamWriter_p.cpp (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// BamWriter_p.cpp (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// ---------------------------------------------------------------------------
// Provides the basic functionality for producing BAM files
// ***************************************************************************
// ---------------------------------------------------------------------------
// Provides the basic functionality for producing BAM files
// ***************************************************************************
memset(pBaseQualities, 0xFF, queryLength); // if missing or '*', fill with invalid qual
else {
for ( size_t i = 0; i < queryLength; ++i )
memset(pBaseQualities, 0xFF, queryLength); // if missing or '*', fill with invalid qual
else {
for ( size_t i = 0; i < queryLength; ++i )