public void testOverlapCigarConsistencyRev() {
final byte[] read =
DnaUtils.encodeString(
DnaUtils.reverseComplement(
"TAGGCGGGTTGCCAA TTAACTTGTA GTCCTTGACA".replaceAll(" ", "")));
final byte[] tmpl =
DnaUtils.encodeString("TAGGG TGGCCAA TTAACTTGTAGTGTGCGTCCTTGACA".replaceAll(" ", ""));
final int[] actions = ActionsHelper.build("==========NNNNNN===============X====BBBX====", 0, 3);
final AlignmentResult ar = new AlignmentResult(read, actions, tmpl);
ar.setIdentifyingInfo(false, true);
// System.out.println("cigar:" + ar.getCigarString(1, true) + " readString:" + ar.readString());
final SAMRecord samrec = new SAMRecord(null);
samrec.setCigarString(ar.getCigarString(true, false));
samrec.setReadString(DnaUtils.reverseComplement(ar.readString()));
samrec.setAttribute(SamUtils.ATTRIBUTE_NUM_MISMATCHES, 2);
samrec.setAlignmentStart(1);
samrec.setFlags(179);
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, false);
assertEquals(
2 * EditDistanceFactory.DEFAULT_SUBSTITUTION_PENALTY,
sv.isAtExpectedRef(tmpl, samrec, null));
}
}
public void testCgTripleInsertRev() {
final String read =
" tagacaaatg ttacaagaccacaggaggggaa".replaceAll(" ", "");
final String temp =
DnaUtils.reverseComplement(
"tagacaaatgtgactggattacaag ccacaggagggggaaa".replaceAll(" ", ""));
final String actions = "==========NNNNNNND=======I============X=";
final AlignmentResult alignment2 =
new AlignmentResult(
DnaUtils.encodeString(read),
ActionsHelper.build(actions, 2, 0),
DnaUtils.encodeString(temp));
alignment2.setIdentifyingInfo(false, true);
alignment2.setRemainingOutput(-2, 1);
assertEquals(0, alignment2.getScore());
assertFalse(alignment2.isFirst());
assertEquals(2, alignment2.getStart());
assertEquals(-2, alignment2.getReadId());
assertEquals(1, alignment2.getReferenceId());
assertEquals(actions, alignment2.getActionsString());
assertEquals(30, alignment2.getMatchCount());
assertEquals(1, alignment2.getDeletionsFromReadCount());
// assertEquals(1, alignment2.getSubstitutionsCount());
assertTrue(alignment2.isReverse());
// assertEquals(3, alignment2.mismatches());
assertEquals("TAGACAAATGTTACAAGACCACAGGAGGGGAA", alignment2.readString());
final String cigar2 = alignment2.getCigarString(true, false);
assertEquals("1=1X12=1I7=1D7N10=", cigar2);
}