/**
* Construct a set of SAM bitwise flags from a GATKRead
*
* @param read read from which to construct the flags
* @return SAM-compliant set of bitwise flags reflecting the properties in the given read
*/
public static int getSAMFlagsForRead(final GATKRead read) {
int samFlags = 0;
if (read.isPaired()) {
samFlags |= SAM_READ_PAIRED_FLAG;
}
if (read.isProperlyPaired()) {
samFlags |= SAM_PROPER_PAIR_FLAG;
}
if (read.isUnmapped()) {
samFlags |= SAM_READ_UNMAPPED_FLAG;
}
if (read.isPaired() && read.mateIsUnmapped()) {
samFlags |= SAM_MATE_UNMAPPED_FLAG;
}
if (!read.isUnmapped() && read.isReverseStrand()) {
samFlags |= SAM_READ_STRAND_FLAG;
}
if (read.isPaired() && !read.mateIsUnmapped() && read.mateIsReverseStrand()) {
samFlags |= SAM_MATE_STRAND_FLAG;
}
if (read.isFirstOfPair()) {
samFlags |= SAM_FIRST_OF_PAIR_FLAG;
}
if (read.isSecondOfPair()) {
samFlags |= SAM_SECOND_OF_PAIR_FLAG;
}
if (read.isSecondaryAlignment()) {
samFlags |= SAM_NOT_PRIMARY_ALIGNMENT_FLAG;
}
if (read.failsVendorQualityCheck()) {
samFlags |= SAM_READ_FAILS_VENDOR_QUALITY_CHECK_FLAG;
}
if (read.isDuplicate()) {
samFlags |= SAM_DUPLICATE_READ_FLAG;
}
if (read.isSupplementaryAlignment()) {
samFlags |= SAM_SUPPLEMENTARY_ALIGNMENT_FLAG;
}
return samFlags;
}
public static boolean isNonPrimary(GATKRead read) {
return read.isSecondaryAlignment() || read.isSupplementaryAlignment() || read.isUnmapped();
}