for ( int i = 0; i < reads.size(); i++ )
{
SAMRecord read = reads.get(i);
if (read.getNotPrimaryAlignmentFlag() ||
read.getDuplicateReadFlag() ||
<BUG>read.getReadUnmappedFlag()

||
read.getMateUnmappedFlag() ||</BUG>
read.getMappingQuality() < MAPPING_QUALITY_THRESHOLD

for ( int i = 0; i < reads.size(); i++ )
{
SAMRecord read = reads.get(i);
if (read.getNotPrimaryAlignmentFlag() ||
read.getDuplicateReadFlag() ||
read.getReadUnmappedFlag() ||
read.getMappingQuality() < MAPPING_QUALITY_THRESHOLD
