/**
* Check to ensure that the alignment makes sense based on the contents of the header.
*
* @param header The SAM file header.
* @param read The read to verify.
* @return true if alignment agrees with header, false otherwise.
*/
public static boolean alignmentAgreesWithHeader(final SAMFileHeader header, final GATKRead read) {
final int referenceIndex = getReferenceIndex(read, header);
// Read is aligned to nonexistent contig
if (!read.isUnmapped() && referenceIndex == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX) {
return false;
}
final SAMSequenceRecord contigHeader = header.getSequence(referenceIndex);
// Read is aligned to a point after the end of the contig
return read.isUnmapped() || read.getStart() <= contigHeader.getSequenceLength();
}
/**
* Returns the reference index in the given header of the read's contig, or {@link
* SAMRecord#NO_ALIGNMENT_REFERENCE_INDEX} if the read is unmapped.
*
* @param read read whose reference index to look up
* @param header SAM header defining contig indices
* @return the reference index in the given header of the read's contig, or {@link
* SAMRecord#NO_ALIGNMENT_REFERENCE_INDEX} if the read is unmapped.
*/
public static int getReferenceIndex(final GATKRead read, final SAMFileHeader header) {
if (read.isUnmapped()) {
return SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX;
}
return header.getSequenceIndex(read.getContig());
}
/**
* 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;
}
/**
* Can the adaptor sequence of read be reliably removed from the read based on the alignment of
* read and its mate?
*
* @param read the read to check
* @return true if it can, false otherwise
*/
public static boolean hasWellDefinedFragmentSize(final GATKRead read) {
if (read.getFragmentLength() == 0)
// no adaptors in reads with mates in another chromosome or unmapped pairs
{
return false;
}
if (!read.isPaired())
// only reads that are paired can be adaptor trimmed
{
return false;
}
if (read.isUnmapped() || read.mateIsUnmapped())
// only reads when both reads are mapped can be trimmed
{
return false;
}
// if ( ! read.isProperlyPaired() )
// // note this flag isn't always set properly in BAMs, can will stop us from
// eliminating some proper pairs
// // reads that aren't part of a proper pair (i.e., have strange alignments) can't
// be trimmed
// return false;
if (read.isReverseStrand() == read.mateIsReverseStrand())
// sanity check on isProperlyPaired to ensure that read1 and read2 aren't on the same strand
{
return false;
}
if (read.isReverseStrand()) {
// we're on the negative strand, so our read runs right to left
return read.getEnd() > read.getMateStart();
} else {
// we're on the positive strand, so our mate should be to our right (his start + insert size
// should be past our start)
return read.getStart() <= read.getMateStart() + read.getFragmentLength();
}
}
public static boolean isNonPrimary(GATKRead read) {
return read.isSecondaryAlignment() || read.isSupplementaryAlignment() || read.isUnmapped();
}