/**
* 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. NULL if the read is unmapped or the mate is mapped to another
* contig.
*/
public static Integer getAdaptorBoundary(final SAMRecord read) {
final int MAXIMUM_ADAPTOR_LENGTH = 8;
final int insertSize =
Math.abs(
read
.getInferredInsertSize()); // the inferred insert size can be negative if the mate
// is mapped before the read (so we take the absolute
// value)
if (insertSize == 0
|| read
.getReadUnmappedFlag()) // no adaptors in reads with mates in another chromosome or
// unmapped pairs
return null;
Integer
adaptorBoundary; // the reference coordinate for the adaptor boundary (effectively the first
// base IN the adaptor, closest to the read)
if (read.getReadNegativeStrandFlag())
adaptorBoundary = read.getMateAlignmentStart() - 1; // case 1 (see header)
else adaptorBoundary = read.getAlignmentStart() + insertSize + 1; // case 2 (see header)
if ((adaptorBoundary < read.getAlignmentStart() - MAXIMUM_ADAPTOR_LENGTH)
|| (adaptorBoundary > read.getAlignmentEnd() + MAXIMUM_ADAPTOR_LENGTH))
adaptorBoundary =
null; // we are being conservative by not allowing the adaptor boundary to go beyond what
// we belive is the maximum size of an adaptor
return adaptorBoundary;
}
/**
* HACK TO CREATE GATKSAMRECORD BASED ONLY A SAMRECORD FOR TESTING PURPOSES ONLY
*
* @param read
*/
public GATKSAMRecord(final SAMRecord read) {
super(read.getHeader());
super.setReferenceIndex(read.getReferenceIndex());
super.setAlignmentStart(read.getAlignmentStart());
super.setReadName(read.getReadName());
super.setMappingQuality(read.getMappingQuality());
// indexing bin done below
super.setCigar(read.getCigar());
super.setFlags(read.getFlags());
super.setMateReferenceIndex(read.getMateReferenceIndex());
super.setMateAlignmentStart(read.getMateAlignmentStart());
super.setInferredInsertSize(read.getInferredInsertSize());
SAMReadGroupRecord samRG = read.getReadGroup();
SAMBinaryTagAndValue samAttr = GATKBin.getReadBinaryAttributes(read);
if (samAttr == null) {
clearAttributes();
} else {
setAttributes(samAttr);
}
if (samRG != null) {
GATKSAMReadGroupRecord rg = new GATKSAMReadGroupRecord(samRG);
setReadGroup(rg);
}
super.setFileSource(read.getFileSource());
super.setReadName(read.getReadName());
super.setCigarString(read.getCigarString());
super.setReadBases(read.getReadBases());
super.setBaseQualities(read.getBaseQualities());
// From SAMRecord constructor: Do this after the above because setCigarString will clear it.
GATKBin.setReadIndexingBin(this, GATKBin.getReadIndexingBin(read));
}
