public void testOverlapCigarConsistency() {
final byte[] read =
DnaUtils.encodeString("GTACTGTGTGCGTCCTTGACATCTA ACCGGCGCCT".replaceAll(" ", ""));
final byte[] tmpl =
DnaUtils.encodeString("GTAGT GTGCGTCCTTGACATCTAAGGATATCGGCGCCTGA".replaceAll(" ", ""));
final int[] actions = ActionsHelper.build("===X=BB====================NNNNN=X========", 0, 3);
final AlignmentResult ar = new AlignmentResult(read, actions, tmpl);
ar.setIdentifyingInfo(true, false);
// System.out.println("cigar:" + ar.getCigarString(1, false) + " readString:" +
// ar.readString());
final SAMRecord samrec = new SAMRecord(null);
samrec.setCigarString(ar.getCigarString(false, false));
samrec.setReadString(ar.readString());
samrec.setAttribute(SamUtils.ATTRIBUTE_NUM_MISMATCHES, 2);
samrec.setReadNegativeStrandFlag(false);
samrec.setFirstOfPairFlag(true);
samrec.setAlignmentStart(1);
samrec.setFlags(67);
final NgsParams params =
new NgsParamsBuilder()
.gapOpenPenalty(EditDistanceFactory.DEFAULT_GAP_OPEN_PENALTY)
.gapExtendPenalty(EditDistanceFactory.DEFAULT_GAP_EXTEND_PENALTY)
.substitutionPenalty(EditDistanceFactory.DEFAULT_SUBSTITUTION_PENALTY)
.unknownsPenalty(0)
.create();
try (MemoryPrintStream mps = new MemoryPrintStream()) {
final SamValidator sv =
new SamValidator(
mps.printStream(), mps.printStream(), true, false, false, false, params, true);
assertEquals(
2 * EditDistanceFactory.DEFAULT_SUBSTITUTION_PENALTY,
sv.isAtExpectedRef(tmpl, samrec, null));
}
}
