@Test(enabled = !DEBUG, dataProvider = "NumAlignedBasesCountingSoftClips") public void testNumAlignedBasesCountingSoftClips(final Cigar cigar, final int expected) { final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "myRead", 0, 1, cigar == null ? 10 : cigar.getReadLength()); read.setCigar(cigar); Assert.assertEquals(AlignmentUtils.getNumAlignedBasesCountingSoftClips(read), expected, "Cigar " + cigar + " failed NumAlignedBasesCountingSoftClips"); }
@Override protected Double getElementForRead(final GATKSAMRecord read, final int refLoc) { final int offset = ReadUtils.getReadCoordinateForReferenceCoordinate( read.getSoftStart(), read.getCigar(), refLoc, ReadUtils.ClippingTail.RIGHT_TAIL, true ); if ( offset == ReadUtils.CLIPPING_GOAL_NOT_REACHED ) return null; // If the offset inside a deletion, it does not lie on a read. if ( AlignmentUtils.isInsideDeletion(read.getCigar(), offset) ) { return INVALID_ELEMENT_FROM_READ; } int readPos = AlignmentUtils.calcAlignmentByteArrayOffset( read.getCigar(), offset, false, 0, 0 ); final int numAlignedBases = AlignmentUtils.getNumAlignedBasesCountingSoftClips( read ); if (readPos > numAlignedBases / 2) readPos = numAlignedBases - (readPos + 1); return (double)readPos; }
@Override protected Double getElementForRead(final GATKSAMRecord read, final int refLoc) { final int offset = ReadUtils.getReadCoordinateForReferenceCoordinate(read.getSoftStart(), read.getCigar(), refLoc, ReadUtils.ClippingTail.RIGHT_TAIL, true); if ( offset == ReadUtils.CLIPPING_GOAL_NOT_REACHED ) return null; // If the offset inside a deletion, it does not lie on a read. if ( AlignmentUtils.isInsideDeletion(read.getCigar(), offset) ) { return INVALID_ELEMENT_FROM_READ; } int readPos = AlignmentUtils.calcAlignmentByteArrayOffset(read.getCigar(), offset, false, 0, 0); final int numAlignedBases = AlignmentUtils.getNumAlignedBasesCountingSoftClips( read ); if (readPos > numAlignedBases / 2) readPos = numAlignedBases - (readPos + 1); return (double)readPos; }