/**
* 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;
}
