/**
* Finds the adaptor boundary around the read and returns the first base inside the adaptor that
* is closest to the read boundary. If the read is in the positive strand, this is the first base
* after the end of the fragment (Picard calls it 'insert'), if the read is in the negative
* strand, this is the first base before the beginning of the fragment.
*
* <p>There are two cases we need to treat here:
*
* <p>1) Our read is in the reverse strand :
*
* <p><----------------------| * |--------------------->
*
* <p>in these cases, the adaptor boundary is at the mate start (minus one)
*
* <p>2) Our read is in the forward strand :
*
* <p>|----------------------> * <----------------------|
*
* <p>in these cases the adaptor boundary is at the start of the read plus the inferred insert
* size (plus one)
*
* @param read the read being tested for the adaptor boundary
* @return the reference coordinate for the adaptor boundary (effectively the first base IN the
* adaptor, closest to the read. CANNOT_COMPUTE_ADAPTOR_BOUNDARY if the read is unmapped or
* the mate is mapped to another contig.
*/
public static int getAdaptorBoundary(final GATKRead read) {
if (!hasWellDefinedFragmentSize(read)) {
return CANNOT_COMPUTE_ADAPTOR_BOUNDARY;
} else if (read.isReverseStrand()) {
return read.getMateStart() - 1; // case 1 (see header)
} else {
final int insertSize =
Math.abs(
read
.getFragmentLength()); // the inferred insert size can be negative if the mate is
// mapped before the read (so we take the absolute value)
return read.getStart() + insertSize + 1; // case 2 (see header)
}
}
/**
* 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();
}
}
/**
* 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;
}
/**
* Returns the read's unclipped start if the read is on the forward strand, or the read's
* unclipped end if the read is on the reverse strand.
*
* @param read read whose stranded unclipped start to retrieve
* @return the read's unclipped start if the read is on the forward strand, or the read's
* unclipped end if the read is on the reverse strand.
*/
public static int getStrandedUnclippedStart(final GATKRead read) {
return read.isReverseStrand() ? read.getUnclippedEnd() : read.getUnclippedStart();
}
