/**
* Creates an empty GATKSAMRecord with the read's header, read group and mate information, but
* empty (not-null) fields: - Cigar String - Read Bases - Base Qualities
*
* <p>Use this method if you want to create a new empty GATKSAMRecord based on another
* GATKSAMRecord
*
* @param read a read to copy the header from
* @return a read with no bases but safe for the GATK
*/
public static GATKSAMRecord emptyRead(GATKSAMRecord read) {
final GATKSAMRecord emptyRead = new GATKSAMRecord(read.getHeader());
emptyRead.setReferenceIndex(read.getReferenceIndex());
emptyRead.setAlignmentStart(0);
emptyRead.setMappingQuality(0);
// setting read indexing bin last
emptyRead.setFlags(read.getFlags());
emptyRead.setMateReferenceIndex(read.getMateReferenceIndex());
emptyRead.setMateAlignmentStart(read.getMateAlignmentStart());
emptyRead.setInferredInsertSize(read.getInferredInsertSize());
emptyRead.setCigarString("");
emptyRead.setReadBases(new byte[0]);
emptyRead.setBaseQualities(new byte[0]);
SAMReadGroupRecord samRG = read.getReadGroup();
emptyRead.clearAttributes();
if (samRG != null) {
GATKSAMReadGroupRecord rg = new GATKSAMReadGroupRecord(samRG);
emptyRead.setReadGroup(rg);
}
GATKBin.setReadIndexingBin(emptyRead, 0);
return emptyRead;
}
/**
* is this base inside the adaptor of the read?
*
* <p>There are two cases to treat here:
*
* <p>1) Read is in the negative strand => Adaptor boundary is on the left tail 2) Read is in the
* positive strand => Adaptor boundary is on the right tail
*
* <p>Note: We return false to all reads that are UNMAPPED or have an weird big insert size
* (probably due to mismapping or bigger event)
*
* @param read the read to test
* @param basePos base position in REFERENCE coordinates (not read coordinates)
* @return whether or not the base is in the adaptor
*/
public static boolean isBaseInsideAdaptor(final GATKSAMRecord read, long basePos) {
Integer adaptorBoundary = getAdaptorBoundary(read);
if (adaptorBoundary == null || read.getInferredInsertSize() > DEFAULT_ADAPTOR_SIZE)
return false;
return read.getReadNegativeStrandFlag()
? basePos <= adaptorBoundary
: basePos >= adaptorBoundary;
}