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));
}
}
public void testCgOverlap() throws Exception {
final SuperCigarValidator validator = new SuperCigarValidator(0);
final SAMRecord samrec = new SAMRecord(null);
samrec.setAlignmentStart(1);
samrec.setCigarString("25=5N10=");
samrec.setReadString("tttgtaggtcggataaggcgttcatccgacacg");
samrec.setBaseQualityString("4316%8883-56+141663,2.3----45/.,2");
samrec.setAttribute(SamUtils.CG_SUPER_CIGAR, "5=2B20=5N10=");
samrec.setAttribute(SamUtils.CG_OVERLAP_QUALITY, "%6");
samrec.setReadNegativeStrandFlag(false);
samrec.setFlags(67);
validator.setData(
samrec,
DnaUtils.encodeString("tttgtgtaggtcggataaggcgttc atccgacacg".replaceAll(" ", "")),
FastaUtils.asciiToRawQuality("4316%%68883-56+141663,2.3----45/.,2"));
validator.setTemplate(DnaUtils.encodeString("tttgtaggtcggataaggcgttcgggggatccgacacg"));
validator.parse();
assertTrue(validator.getInvalidReason(), validator.isValid());
samrec.setCigarString("3=1X21=5N10=");
samrec.setReadString("tttataggtcggataaggcgttcatccgacacg");
samrec.setBaseQualityString("4316%8883-56+141663,2.3----45/.,2");
samrec.setAttribute(SamUtils.CG_SUPER_CIGAR, "5=2B1X19=5N10=");
samrec.setAttribute(SamUtils.CG_READ_DELTA, "A");
validator.setData(
samrec,
DnaUtils.encodeString("tttgtataggtcggataaggcgttc atccgacacg".replaceAll(" ", "")),
FastaUtils.asciiToRawQuality("4316%%68883-56+141663,2.3----45/.,2"));
validator.parse();
assertTrue(validator.getInvalidReason(), validator.isValid());
}
public void testMismatchFailures() throws Exception {
final SuperCigarValidator validator = new SuperCigarValidator(0);
final SAMRecord samrec = new SAMRecord(null);
samrec.setAlignmentStart(1);
samrec.setCigarString("2=1X13=5N20=");
samrec.setReadString("GACGCCGAGGAAAAACAGGCGGATCGTCAGGAGTT");
samrec.setAttribute(SamUtils.CG_SUPER_CIGAR, "2=1X13=5N20=");
samrec.setBaseQualityString("4316%%68883-56+141663,2.3----45/.,2");
samrec.setFlags(73);
validator.setData(
samrec,
DnaUtils.encodeString("GACGCCGAGG AAAAACAGGCGGATCGTCAGGAGTT".replaceAll(" ", "")),
FastaUtils.asciiToRawQuality("4316%%68883-56+141663,2.3----45/.,2"));
validator.setTemplate(DnaUtils.encodeString("GAGGCCGAGGGGGGGAAAAACAGGCGGATCGTCAGGAGTT"));
try {
validator.parse();
assertFalse(validator.isValid());
assertTrue(
validator.getInvalidReason(),
validator
.getInvalidReason()
.contains("Read delta (" + SamUtils.CG_READ_DELTA + ") too short, "));
} catch (final AssertionError e) {
assertEquals("readDelta.len=0 but should be 1", e.getMessage());
}
samrec.setAttribute(SamUtils.CG_READ_DELTA, "T");
validator.setData(
samrec,
DnaUtils.encodeString("GACGCCGAGG AAAAACAGGCGGATCGTCAGGAGTT".replaceAll(" ", "")),
FastaUtils.asciiToRawQuality("4316%%68883-56+141663,2.3----45/.,2"));
validator.parse();
assertFalse(validator.isValid());
assertTrue(
validator.getInvalidReason(),
validator
.getInvalidReason()
.contains(SamUtils.CG_READ_DELTA + " value: T does not match read value: C"));
validator.setData(
samrec,
DnaUtils.encodeString("GAGGCCGAGG AAAAACAGGCGGATCGTCAGGAGTT".replaceAll(" ", "")),
FastaUtils.asciiToRawQuality("4316%%68883-56+141663,2.3----45/.,2"));
validator.parse();
assertFalse(validator.isValid());
assertTrue(
validator.getInvalidReason(), validator.getInvalidReason().contains("Expected mismatch"));
samrec.setAlignmentStart(5);
samrec.setCigarString("4=1I5=7N25=");
samrec.setReadString("CTGTGGCATCGGGGGACCTGGGGCCCTCNCTGAGT");
samrec.setAttribute(SamUtils.CG_SUPER_CIGAR, "4=1I5=7N25=");
samrec.setAttribute(SamUtils.CG_READ_DELTA, "A");
validator.setData(
samrec,
DnaUtils.encodeString("CTGTGGCATC GGGGGACCTGGGGCCCTCNCTGAGT".replaceAll(" ", "")),
FastaUtils.asciiToRawQuality("4316%%68883-56+141663,2.3----45/.,2"));
validator.setTemplate(
DnaUtils.encodeString(
"TGTTCTGTG CATCTTCCCTTGGGGGACCTGNGGCCCTCACTGAGTGGGTCCTCCATGGGTGACTGGTGA"));
validator.parse();
assertFalse(validator.getInvalidReason(), validator.isValid());
assertTrue(
validator.getInvalidReason(),
validator
.getInvalidReason()
.contains("SDF read insert: G does not match SAM " + SamUtils.CG_READ_DELTA + ": A,"));
samrec.setAlignmentStart(2);
samrec.setCigarString("23=6N10=");
samrec.setReadString("CTTCAGCGATGGAGAAACTCGGGTGTCTACGTA");
samrec.setAttribute(SamUtils.CG_SUPER_CIGAR, "5=2B20=6N10=");
samrec.setAttribute(SamUtils.CG_READ_DELTA, null);
samrec.setAttribute(SamUtils.CG_OVERLAP_QUALITY, "%6");
samrec.setBaseQualityString("4316%8883-56+141663,2.3----45/.,2");
samrec.setFlags(179);
validator.setData(
samrec,
DnaUtils.encodeString("TACGTAGACA CCCGAGTGTCTCCATCGCTGTGAAG".replaceAll(" ", "")),
FastaUtils.asciiToRawQuality("2,./54----3.2,366141+65-38886%%6134"));
validator.setTemplate(
DnaUtils.encodeString("GCTTCAGCGATGGAGAAACTCGGGAAGTCGTGTCTACGTAGAACGTAGTT"));
validator.parse();
assertFalse(validator.getInvalidReason(), validator.isValid());
assertTrue(
validator.getInvalidReason(),
validator.getInvalidReason().contains("Expected match, SDF read=C, template=A,"));
samrec.setAlignmentStart(1);
samrec.setCigarString("10M5N25M");
samrec.setReadString("GAGGCCGAGGCAGGCGGATCGTCAGGAGTTAAAAA");
samrec.setAttribute(SamUtils.CG_SUPER_CIGAR, "10=5N25=");
samrec.setAttribute(SamUtils.CG_OVERLAP_QUALITY, null);
samrec.setBaseQualityString("4316%668883-56+141663,2.3----45/.,2");
samrec.setFlags(73);
validator.setData(
samrec,
DnaUtils.encodeString("GAGGCCGAGG CAGGCGGATCGTCAGGAGTTAAAAA".replaceAll(" ", "")),
FastaUtils.asciiToRawQuality("4316%%68883-56+141663,2.3----45/.,2"));
validator.setTemplate(DnaUtils.encodeString("GAGGCCGAGGGGGGGCAGGCGGATCGTCAGGAGTTAAAAA"));
validator.parse();
assertFalse(validator.getInvalidReason(), validator.isValid());
assertTrue(
validator.getInvalidReason(),
validator.getInvalidReason().contains("SDF and SAM qualities don't match,"));
samrec.setAlignmentStart(1);
samrec.setCigarString("25=5N10=");
samrec.setReadString("tttgtaggtcggataaggcgttcatccgacacg");
samrec.setBaseQualityString("4316%8883-56+141663,2.3----45/.,2");
samrec.setAttribute(SamUtils.CG_SUPER_CIGAR, "5=2B20=5N10=");
samrec.setAttribute(SamUtils.CG_OVERLAP_QUALITY, "6");
samrec.setReadNegativeStrandFlag(false);
samrec.setFlags(67);
try {
validator.setData(
samrec,
DnaUtils.encodeString("tttgtgtaggtcggataaggcgttc atccgacacg".replaceAll(" ", "")),
FastaUtils.asciiToRawQuality("4316%%68883-56+141663,2.3----45/.,2"));
fail();
} catch (final BadSuperCigarException iae) {
assertTrue(
iae.getMessage(),
iae.getMessage()
.contains("SAM record qualities plus XQ not expected length. Was: 34 expected: 35"));
}
samrec.setAlignmentStart(1);
samrec.setCigarString("25=5N10=");
samrec.setReadString("tttgtaggtcggataaggcgttcatccgacacg");
samrec.setBaseQualityString("4316%%68883-56+141663,2.3----45/.,2");
samrec.setAttribute(SamUtils.CG_SUPER_CIGAR, "5=2B20=5N10=");
samrec.setAttribute(SamUtils.CG_OVERLAP_QUALITY, null);
samrec.setReadNegativeStrandFlag(false);
samrec.setFlags(67);
validator.setTemplate(DnaUtils.encodeString("tttgtaggtcggataaggcgttcgggggatccgacacg"));
validator.setData(
samrec,
DnaUtils.encodeString("tttgtgtaggtcggataaggcgttc atccgacacg".replaceAll(" ", "")),
FastaUtils.asciiToRawQuality("4316%%68883-56+141663,2.3----45/.,2"));
validator.parse();
assertFalse(validator.getInvalidReason(), validator.isValid());
assertTrue(
validator.getInvalidReason(),
validator
.getInvalidReason()
.contains(
"Overlap described but no " + SamUtils.CG_OVERLAP_QUALITY + " field present"));
}
@Override
public void setReadNegativeStrandFlag(final boolean flag) {
if (isStrandless())
throw new IllegalStateException("Cannot set the strand of a strandless read");
super.setReadNegativeStrandFlag(flag);
}