public void testOverlapPastStartPosition() throws Exception {
final SuperCigarValidator validator = new SuperCigarValidator(0);
final SAMRecord samrec = new SAMRecord(null);
samrec.setAlignmentStart(3);
samrec.setCigarString("2=2I16=6N10=");
samrec.setReadString("ATAAGAAGGAGTGGCACTTCCCTCAGCTCA");
samrec.setAttribute(SamUtils.CG_SUPER_CIGAR, "2=2I1=4B1X1=1I17=6N10=");
samrec.setBaseQualityString("20001.1-+,8/0/41373,1751662362");
samrec.setAttribute(SamUtils.CG_READ_DELTA, "AAGG");
samrec.setAttribute(SamUtils.CG_OVERLAP_QUALITY, ").,1/");
samrec.setAttribute(SamUtils.ATTRIBUTE_ALIGNMENT_SCORE, 6);
samrec.setFlags(179);
final String rawread = "TGAGCTGAGG GAAGTGCCACTCCTTCACTCCTTAT".replaceAll(" ", "");
final String rawqual = "2632661571 ,37314/0/8,+-1./1,.)10002".replaceAll(" ", "");
validator.setData(
samrec, DnaUtils.encodeString(rawread), FastaUtils.asciiToRawQuality(rawqual));
validator.setTemplate(
DnaUtils.encodeString(
"TCAT GAAGGAGTGGCACTTCCACCTGCCTCAGCTCATGCGTGATATCCAGG".replaceAll(" ", "")));
// ATAAGAAGGAGTGGCACTTCCCTCAGCTCA
// ATAAG
// TCA TGAAGGAGTGGCACTTCCACCTGCCTCAGCTCATGCGTGATATCCAGG
// GAGTGAAGGAGTGGCACTTC CCTCAGCTCA
validator.parse();
assertTrue(validator.getInvalidReason(), validator.isValid());
}
public void testUnknownPenalty() throws Exception {
final SuperCigarValidator validator = new SuperCigarValidator(1);
final SAMRecord samrec = new SAMRecord(null);
samrec.setAlignmentStart(1);
samrec.setCigarString("8=1X14=5N10=");
samrec.setReadString("AGCCCCCNTACGTAAATAAGACATCACGATGATCA");
samrec.setAttribute(SamUtils.CG_SUPER_CIGAR, "7=1R1X1T15=5N10=");
samrec.setBaseQualityString("4316%%68883-56+141663,2.3----45/.,2");
samrec.setAttribute(SamUtils.CG_READ_DELTA, "TA");
samrec.setAttribute(SamUtils.ATTRIBUTE_ALIGNMENT_SCORE, 1);
samrec.setFlags(67);
validator.setData(
samrec,
DnaUtils.encodeString("AGCCCCCNTACGTAAATAAGACATC ACGATGATCA".replaceAll(" ", "")),
FastaUtils.asciiToRawQuality("4316%%68883-56+141663,2.3----45/.,2"));
validator.setTemplate(DnaUtils.encodeString("AGCCCCCACNCGTAAATAAGACATCTTTTTACGATGATCA"));
validator.parse();
assertFalse(validator.getInvalidReason(), validator.isValid());
assertEquals(
validator.getInvalidReason(),
"Super cigar alignment score was 3, but AS attribute was 1",
validator.getInvalidReason());
samrec.setAttribute(SamUtils.ATTRIBUTE_ALIGNMENT_SCORE, 3);
validator.setData(
samrec,
DnaUtils.encodeString("AGCCCCCNTACGTAAATAAGACATC ACGATGATCA".replaceAll(" ", "")),
FastaUtils.asciiToRawQuality("4316%%68883-56+141663,2.3----45/.,2"));
validator.setTemplate(DnaUtils.encodeString("AGCCCCCACNCGTAAATAAGACATCTTTTTACGATGATCA"));
validator.parse();
assertTrue(validator.getInvalidReason(), validator.isValid());
}
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 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);
}
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 testDegenerate() 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(" "),
FastaUtils.asciiToRawQuality("4316%%68883-56+141663,2.3----45/.,2"));
validator.setTemplate(DnaUtils.encodeString("GAGGCCGAGGGGGGGAAAAACAGGCGGATCGTCAGGAGTT"));
validator.parse();
assertFalse(validator.isValid());
samrec.setFlags(115);
validator.setData(
samrec,
DnaUtils.encodeString(" "),
FastaUtils.asciiToRawQuality("4316%%68883-56+141663,2.3----45/.,2"));
validator.parse();
assertFalse(validator.isValid());
}
void checkFastq(SequencesIterator it, String name, String read) throws IOException {
final byte[] readBytes = new byte[it.currentLength()];
it.readCurrent(readBytes);
assertEquals(name, it.currentName());
assertEquals(read, DnaUtils.bytesToSequenceIncCG(readBytes));
it.readCurrentQuality(readBytes);
}
public void testInvalidSoftClipping() {
final byte[] read =
DnaUtils.encodeString("GAGGGTTAGG GTGAGGGTTTGGGTTAGGGTATTAG".replaceAll(" ", ""));
byte[] tmpl = DnaUtils.encodeString("GAGGGTTAGGGTTAGGGTGAGGGTTAGGGTTAGGG".replaceAll(" ", ""));
int[] actions = ActionsHelper.build("==========NNNNNN=========X==========B=====", 0, 3);
AlignmentResult ar = new AlignmentResult(read, actions, tmpl);
assertEquals("10=6N9=1X9=5S", ar.getCigarString(false, false));
// GAGGGTTAGG .GTGAGGGTTTGGGTTAGGGTATTAG
tmpl =
DnaUtils.encodeString("AAAAAAAAAAGAGGGTTAGGGTTAGGGTGAGGGTTAGGGTTAGGG".replaceAll(" ", ""));
actions = ActionsHelper.build("==========NNNNNN=========X==========B=====", 10, 3);
ar = new AlignmentResult(read, actions, tmpl);
assertEquals("10=6N9=1X9=5S", ar.getCigarString(false, false));
//
// assertEquals("gagggttagg......gtgagggtttgggttagggattag\tgagggttagggttagggtgagggttagggttagggnnnnn\t|||||||||| ||||||||| ||||||||| ", ar.tabularString());
}
public void test4Gap() throws Exception {
//
// CCATTCAGTTGGAGACGTTGTGGACCTGACGCCTCTGCTCTTGCAAGTCAGGACAT
// 24106 67 paolo-bac 420 255 16=4I1=1I2=4N10= paolo-bac
// 735 315 CAGTTGGAGACGTTGTGNATGTGNACGCCTCTGC 213.3/22..103350/!2,2+/!14/-+-4//5
// AS:i:6 NM:i:5 MQ:i:255 XU:Z:5=1B12=4I1=1I2=4N10= XQ:Z:1 XR:Z:GNATT
// XA:i:10 IH:i:1
final SuperCigarValidator validator = new SuperCigarValidator(0);
final SAMRecord samrec = new SAMRecord(null);
samrec.setAlignmentStart(6);
samrec.setCigarString("16=4I1=1I2=4N10=");
samrec.setReadString("CAGTTGGAGACGTTGTGNATGTGNACGCCTCTGC");
samrec.setBaseQualityString("213.3/22..103350/!2,2+/!14/-+-4//5");
samrec.setAttribute(SamUtils.CG_SUPER_CIGAR, "5=1B12=4I1=1I2=4N10=");
samrec.setAttribute(SamUtils.CG_OVERLAP_QUALITY, "1");
samrec.setAttribute(SamUtils.CG_READ_DELTA, "GNATT");
samrec.setAttribute(SamUtils.ATTRIBUTE_ALIGNMENT_SCORE, 7);
samrec.setFlags(67);
// CAGTT GGAGACGTTGTGNATG T GN ACGCCTCTGC
validator.setData(
samrec,
DnaUtils.encodeString("CAGTTTGGAGACGTTGTGNATGTGN ACGCCTCTGC".replaceAll(" ", "")),
FastaUtils.asciiToRawQuality(
"213.31/22..103350/!2,2+/!14/-+-4//5")); // tttgt aggtcggataaggcgttcgg atccgacacg
validator.setTemplate(
DnaUtils.encodeString("CCATTCAGTTGGAGACGTTGTGGACCTGACGCCTCTGCTCTTGCAAGTCAGGACAT"));
validator.parse();
assertTrue(validator.getInvalidReason(), validator.isValid());
samrec.setAttribute(SamUtils.ATTRIBUTE_ALIGNMENT_SCORE, 6);
validator.setData(
samrec,
DnaUtils.encodeString("CAGTTTGGAGACGTTGTGNATGTGN ACGCCTCTGC".replaceAll(" ", "")),
FastaUtils.asciiToRawQuality(
"213.31/22..103350/!2,2+/!14/-+-4//5")); // tttgt aggtcggataaggcgttcgg atccgacacg
validator.setTemplate(
DnaUtils.encodeString("CCATTCAGTTGGAGACGTTGTGGACCTGACGCCTCTGCTCTTGCAAGTCAGGACAT"));
validator.parse();
assertFalse(validator.getInvalidReason(), validator.isValid());
assertEquals(
"Super cigar alignment score was 7, but AS attribute was 6", validator.getInvalidReason());
}
public void testReadMeNoDirectory() throws IOException {
final CompressedMemorySequencesReader msr =
new CompressedMemorySequencesReader(
new byte[][] {DnaUtils.encodeArray("acgtcacgtcacgtcacgtcacgtcacgtcacgtc".getBytes())},
new String[] {"seq1"},
new long[] {35},
35,
35,
SequenceType.DNA);
assertNull(msr.getReadMe());
}
public void testArrayPrereadNames() {
Diagnostic.setLogStream();
final String seqString = "acgtcacgtcacgtcacgtcacgtcacgtcacgtc";
new MyMemorySequencesReader(
new byte[][] {DnaUtils.encodeArray(seqString.getBytes())},
new String[] {"seq1"},
new long[] {35},
35,
35,
SequenceType.DNA);
}
public void testCGOverlapWithDeletion2() throws Exception {
// check that it is OK to not provide XQ if the overlap is deleted from the template
final SuperCigarValidator validator = new SuperCigarValidator(0);
final SAMRecord samrec = new SAMRecord(null);
// GGGCCTGCAC
// DDD
// BB
// TGGCCAAGGAGCTGTGTGA
// GGGCCTGCACCTGGCCAAGGAGCTGTGTGA
//
samrec.setAlignmentStart(1);
samrec.setCigarString("10=1D19=");
samrec.setReadString("GGGCCTGCACTGGCCAAGGAGCTGTGTGA");
samrec.setAttribute(SamUtils.CG_SUPER_CIGAR, "10=3D2B19=");
samrec.setAttribute(SamUtils.ATTRIBUTE_ALIGNMENT_SCORE, 4);
samrec.setBaseQualityString("/////////////////////////////");
samrec.setFlags(131);
final byte[] sdfRead =
DnaUtils.encodeString("GGGCCTGCACTGGCCAAGGAGCTGTGTGA".replaceAll(" ", ""));
final byte[] sdfQualities = FastaUtils.asciiToRawQuality("/////////////////////////////");
validator.setData(samrec, sdfRead, sdfQualities);
validator.setTemplate(DnaUtils.encodeString("GGGCCTGCACCTGGCCAAGGAGCTGTGTGA"));
validator.parse();
assertTrue(validator.getInvalidReason(), validator.isValid());
// theoretical alignment that probably isn't handled:
// ACG
// DDD
// G
// BB
// C
// D
// TACGTACGTACGT
// ACGTACGTACGTACGTACGT
// The overlap actually has a match on either side of it, however no template position is
// repeated
// in a match or mismatch so would not result in a flattened read needing an XQ field.
}
@Override
public String readString() {
return DnaUtils.bytesToSequenceIncCG(mReferenceBytes);
}
public void testCGOverlapWithDeletion() throws Exception {
// check that it is OK to not provide XQ if the overlap is deleted from the template
final SuperCigarValidator validator = new SuperCigarValidator(0);
final SAMRecord samrec = new SAMRecord(null);
samrec.setAlignmentStart(1);
samrec.setCigarString("29=");
samrec.setReadString("AGGCAGGTAGATCATGAGGTGAAGAGATC");
samrec.setAttribute(SamUtils.CG_SUPER_CIGAR, "19=2B2D10=");
samrec.setAttribute(SamUtils.ATTRIBUTE_ALIGNMENT_SCORE, 3);
samrec.setBaseQualityString("/////////////////////////////");
samrec.setFlags(179);
final byte[] sdfRead =
DnaUtils.encodeString("GATCTCTTCACCTCATGATCTACCTGCCT".replaceAll(" ", ""));
final byte[] sdfQualities = FastaUtils.asciiToRawQuality("/////////////////////////////");
validator.setData(samrec, sdfRead, sdfQualities);
validator.setTemplate(DnaUtils.encodeString("AGGCAGGTAGATCATGAGGTGAAGAGATC"));
validator.parse();
assertTrue(validator.getInvalidReason(), validator.isValid());
samrec.setAttribute(SamUtils.CG_SUPER_CIGAR, "19=2B2N10=");
samrec.setAttribute(SamUtils.ATTRIBUTE_ALIGNMENT_SCORE, 0);
validator.setData(samrec, sdfRead, sdfQualities);
validator.parse();
assertTrue(validator.getInvalidReason(), validator.isValid());
samrec.setAttribute(SamUtils.CG_SUPER_CIGAR, "19=2B2H10=");
samrec.setAttribute(SamUtils.ATTRIBUTE_ALIGNMENT_SCORE, 0);
validator.setData(samrec, sdfRead, sdfQualities);
validator.parse();
assertTrue(validator.getInvalidReason(), validator.isValid());
samrec.setCigarString("19=2D8=");
samrec.setReadString(
"TGGCAGGTAGATCATGAGGAAGAGATC"); // <- this doesn't seem to be checked by anything
samrec.setBaseQualityString("/////////////////////////////");
samrec.setAttribute(SamUtils.CG_SUPER_CIGAR, "19=2B1X1=2D8=");
samrec.setAttribute(SamUtils.ATTRIBUTE_ALIGNMENT_SCORE, 4);
samrec.setAttribute(SamUtils.CG_READ_DELTA, "T");
validator.setData(samrec, sdfRead, sdfQualities);
validator.parse();
assertFalse(validator.isValid());
assertTrue(
validator.getInvalidReason(),
validator
.getInvalidReason()
.contains("Overlap described but no XQ field present in SAM record"));
samrec.setReadString("AGGCAGGTAGATCATGAGGAAGAGATC");
samrec.setBaseQualityString("/////////////////////////////");
samrec.setAttribute(SamUtils.CG_SUPER_CIGAR, "19=2B1X1=3X3=2X");
samrec.setAttribute(SamUtils.CG_READ_DELTA, "TAAGTC");
samrec.setAttribute(SamUtils.ATTRIBUTE_ALIGNMENT_SCORE, 6);
validator.setData(samrec, sdfRead, sdfQualities);
validator.parse();
assertFalse(validator.isValid());
assertTrue(
validator.getInvalidReason(),
validator
.getInvalidReason()
.contains("Overlap described but no XQ field present in SAM record"));
}
public void testMismatches() {
AlignmentResult ar =
new AlignmentResult(
DnaUtils.encodeString("acgtacgta"),
ActionsHelper.build("=========", 0, 0),
DnaUtils.encodeString("acgtacgta"));
assertEquals(0, ar.mismatches());
assertEquals("ACGTACGTA", ar.readString());
ar.setIdentifyingInfo(false, true);
assertEquals("ACGTACGTA", ar.readString());
ar =
new AlignmentResult(
DnaUtils.encodeString("acgtacgta"),
ActionsHelper.build("X=======X", 0, 0),
DnaUtils.encodeString("atgttcgta"));
assertEquals(2, ar.mismatches());
ar =
new AlignmentResult(
DnaUtils.encodeString("acgtacgta"),
ActionsHelper.build("=X==X====", 0, 0),
DnaUtils.encodeString("atgttcgta"));
assertEquals(2, ar.mismatches());
assertEquals("ACGTACGTA", ar.readString());
ar.setIdentifyingInfo(false, true);
assertEquals("ACGTACGTA", ar.readString());
ar =
new AlignmentResult(
DnaUtils.encodeString("acgcgta"),
ActionsHelper.build("===DD====", 0, 3),
DnaUtils.encodeString("acgtacgta"));
assertEquals(2, ar.mismatches());
assertEquals("ACGCGTA", ar.readString());
ar.setIdentifyingInfo(false, true);
assertEquals("ACGCGTA", ar.readString());
ar =
new AlignmentResult(
DnaUtils.encodeString("acgcgta"),
ActionsHelper.build("===DD====", 0, 3),
DnaUtils.encodeString("acgt"));
assertEquals(6, ar.mismatches());
assertEquals("ACGCGTA", ar.readString());
ar =
new AlignmentResult(
DnaUtils.encodeString("acgcgta"),
ActionsHelper.build("===DD====", 0, 3),
DnaUtils.encodeString("acgtacgt"));
assertEquals(3, ar.mismatches());
assertEquals("ACGCGTA", ar.readString());
ar =
new AlignmentResult(
DnaUtils.encodeString("acgcgta"),
ActionsHelper.build("===DD====", 0, 3),
DnaUtils.encodeString("acgtacgt"));
assertEquals(3, ar.mismatches());
assertEquals("ACGCGTA", ar.readString());
ar =
new AlignmentResult(
DnaUtils.encodeString("acgtacgta"),
ActionsHelper.build("===II====", 0, 3),
DnaUtils.encodeString("acgcgta"));
assertEquals(2, ar.mismatches());
assertEquals("ACGTACGTA", ar.readString());
ar.setIdentifyingInfo(false, true);
assertEquals("ACGTACGTA", ar.readString());
ar =
new AlignmentResult(
DnaUtils.encodeString("acgtacgta"),
ActionsHelper.build("===II====", 0, 3),
DnaUtils.encodeString("acg"));
assertEquals(4, ar.mismatches());
assertEquals("ACGTACGTA", ar.readString());
ar =
new AlignmentResult(
DnaUtils.encodeString("acgtacgta"),
ActionsHelper.build("===II====", 0, 3),
DnaUtils.encodeString("acgcgt"));
assertEquals(3, ar.mismatches());
assertEquals("ACGTACGTA", ar.readString());
}
public void testSimpleMatches() throws Exception {
final SuperCigarValidator validator = new SuperCigarValidator(0);
final SAMRecord samrec = new SAMRecord(null);
samrec.setAlignmentStart(1);
samrec.setCigarString("10M5N25M");
samrec.setReadString("GAGGCCGAGGCAGGCGGATCGTCAGGAGTTAAAAA");
samrec.setAttribute(SamUtils.CG_SUPER_CIGAR, "10=5N25=");
samrec.setAttribute(SamUtils.ATTRIBUTE_ALIGNMENT_SCORE, 0);
samrec.setBaseQualityString("4316%%68883-56+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();
assertTrue(validator.getInvalidReason(), validator.isValid());
samrec.setCigarString("2=1X7=5N25=");
samrec.setReadString("GACGCCGAGGCAGGCGGATCGTCAGGAGTTAAAAA");
samrec.setAttribute(SamUtils.CG_SUPER_CIGAR, "2=1X7=5N25=");
samrec.setAttribute(SamUtils.CG_READ_DELTA, "C");
validator.setData(
samrec,
DnaUtils.encodeString("GACGCCGAGG CAGGCGGATCGTCAGGAGTTAAAAA".replaceAll(" ", "")),
FastaUtils.asciiToRawQuality("4316%%68883-56+141663,2.3----45/.,2"));
validator.parse();
assertFalse(validator.getInvalidReason(), validator.isValid());
samrec.setAttribute(SamUtils.ATTRIBUTE_ALIGNMENT_SCORE, null);
validator.setData(
samrec,
DnaUtils.encodeString("GACGCCGAGG CAGGCGGATCGTCAGGAGTTAAAAA".replaceAll(" ", "")),
FastaUtils.asciiToRawQuality("4316%%68883-56+141663,2.3----45/.,2"));
validator.parse();
assertTrue(validator.getInvalidReason(), validator.isValid());
samrec.setAlignmentStart(5);
samrec.setCigarString("4=1D6=5N25=");
samrec.setReadString("CTGTCATCTTACCTGGGGCCCTCNCTGAGTGGGTC");
samrec.setAttribute(SamUtils.CG_SUPER_CIGAR, "4=1D6=5N25=");
samrec.setAttribute(SamUtils.CG_READ_DELTA, null);
samrec.setAttribute(SamUtils.ATTRIBUTE_ALIGNMENT_SCORE, 2);
validator.setData(
samrec,
DnaUtils.encodeString("CTGTCATCTT ACCTGGGGCCCTCNCTGAGTGGGTC".replaceAll(" ", "")),
FastaUtils.asciiToRawQuality("4316%%68883-56+141663,2.3----45/.,2"));
validator.setTemplate(
DnaUtils.encodeString("TGTTCTGTGCATCTTCCCTTACCTGNGGCCCTCACTGAGTGGGTCCTCCATGGGTGACTGGTGA"));
validator.parse();
assertTrue(validator.getInvalidReason(), validator.isValid());
samrec.setAlignmentStart(5);
samrec.setCigarString("4=1I5=7N25=");
samrec.setReadString("CTGTAGCATCACCTGGGGCCCTCNCTGAGTGGGTC");
samrec.setAttribute(SamUtils.CG_SUPER_CIGAR, "4=1I5=7N25=");
samrec.setAttribute(SamUtils.CG_READ_DELTA, "A");
samrec.setAttribute(SamUtils.ATTRIBUTE_ALIGNMENT_SCORE, null);
validator.setData(
samrec,
DnaUtils.encodeString("CTGTAGCATC ACCTGGGGCCCTCNCTGAGTGGGTC".replaceAll(" ", "")),
FastaUtils.asciiToRawQuality("4316%%68883-56+141663,2.3----45/.,2"));
validator.parse();
assertTrue(validator.getInvalidReason(), validator.isValid());
samrec.setAlignmentStart(5);
samrec.setCigarString("4=2D6=5N25=");
samrec.setReadString("CTGTCATCTTACCTGGGGCCCTCNCTGAGTGGGTC");
samrec.setAttribute(SamUtils.CG_SUPER_CIGAR, "4=2D6=5N25=");
samrec.setAttribute(SamUtils.CG_READ_DELTA, null);
samrec.setAttribute(SamUtils.ATTRIBUTE_ALIGNMENT_SCORE, 3);
validator.setData(
samrec,
DnaUtils.encodeString("CTGTCATCTT ACCTGGGGCCCTCNCTGAGTGGGTC".replaceAll(" ", "")),
FastaUtils.asciiToRawQuality("4316%%68883-56+141663,2.3----45/.,2"));
validator.setTemplate(
DnaUtils.encodeString("TGTTCTGTGGCATCTTCCCTTACCTGNGGCCCTCACTGAGTGGGTCCTCCATGGGTGACTGGTGA"));
validator.parse();
assertTrue(validator.getInvalidReason(), validator.isValid());
// reverse complement
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.setAttribute(SamUtils.ATTRIBUTE_ALIGNMENT_SCORE, 0);
samrec.setBaseQualityString("4316%8883-56+141663,2.3----45/.,2");
samrec.setFlags(179);
validator.setData(
samrec,
DnaUtils.encodeString("TACGTAGACA CCCGAGTTTCTCCATCGCTGTGAAG".replaceAll(" ", "")),
FastaUtils.asciiToRawQuality("2,./54----3.2,366141+65-38886%%6134"));
validator.setTemplate(
DnaUtils.encodeString("GCTTCAGCGATGGAGAAACTCGGGAAGTCGTGTCTACGTAGAACGTAGTT"));
validator.parse();
assertTrue(validator.getInvalidReason(), validator.isValid());
}
private byte[] getSequence(final String s) {
return DnaUtils.encodeArray(s.replaceAll(" ", "").getBytes());
}
public void testReadString() {
AlignmentResult ar =
new AlignmentResult(
DnaUtils.encodeString("acgtacgta"),
ActionsHelper.build("=========", 0, 0),
"".getBytes());
ar.setIdentifyingInfo(true, false);
assertEquals("ACGTACGTA", ar.readString());
ar =
new AlignmentResult(
DnaUtils.encodeString("acgtacg"),
ActionsHelper.build("==BB==R==", 0, 3),
"".getBytes());
ar.setIdentifyingInfo(true, false);
assertEquals("ACACG", ar.readString());
ar =
new AlignmentResult(
DnaUtils.encodeString("acgtacgt"),
ActionsHelper.build("==BB=I==T=", 0, 3),
"".getBytes());
ar.setIdentifyingInfo(true, false);
assertEquals("ACCGT", ar.readString());
ar =
new AlignmentResult(
DnaUtils.encodeString("acgtacg"),
ActionsHelper.build("===BB====", 0, 3),
"".getBytes());
ar.setIdentifyingInfo(false, false);
assertEquals("ATACG", ar.readString());
ar =
new AlignmentResult(
DnaUtils.encodeString("acgtacgt"),
ActionsHelper.build("==I=BBN==N==", 0, 3),
"".getBytes());
ar.setIdentifyingInfo(false, false);
assertEquals("AACGT", ar.readString());
ar =
new AlignmentResult(
DnaUtils.encodeString("acgtacg"),
ActionsHelper.build("==D=BB====", 0, 3),
"".getBytes());
ar.setIdentifyingInfo(false, false);
assertEquals("ACTACG", ar.readString());
ar =
new AlignmentResult(
DnaUtils.encodeString("acgtacg"),
ActionsHelper.build("==N=BB====", 0, 3),
"".getBytes());
ar.setIdentifyingInfo(false, false);
assertEquals("ACTACG", ar.readString());
final int[] actions = ActionsHelper.build("==I=========D==", 0, 3);
ActionsHelper.softClip(actions, true, 3, 0);
ActionsHelper.softClip(actions, false, 2, 1);
ar = new AlignmentResult(DnaUtils.encodeString("AATAAAAAAAAAGG"), actions, "".getBytes());
ar.setIdentifyingInfo(false, false);
assertEquals("AATAAAAAAAAAGG", ar.readString());
}
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"));
}
public void testQualities() throws Exception {
// first, non-rc
/*237726 67 simulatedSequence1 3 255 22=6N10= = 170 167 TGCCCCCCTGAGAATGAATGTTGGACGAAATA )*N\S\7@*`[4DRA8VKE-JF:KP0<D:/"K AS:i:0 NM:i:0 MQ:i:255 XU:Z:5=3B20=6N10=
TGCCCCCCCCCTGAGAATGAATGTTGGACGAAATA
)*N\SV55\7@*`[4DRA8VKE-JF:KP0<D:/"K
XQ:Z:V55 XA:i:1 IH:i:1*/
final SuperCigarValidator validator = new SuperCigarValidator(0);
final SAMRecord samrec = new SAMRecord(null);
samrec.setAlignmentStart(3);
samrec.setCigarString("22=6N10=");
samrec.setReadString("tgcccccctgagaatgaatgttggacgaaata");
samrec.setBaseQualityString(")*N!S!7@*`[4DRA8VKE-JF:KP0<D:/!K");
samrec.setAttribute(SamUtils.CG_SUPER_CIGAR, "5=3B20=6N10=");
samrec.setAttribute(SamUtils.CG_OVERLAP_QUALITY, "V55");
samrec.setFlags(67);
validator.setData(
samrec,
DnaUtils.encodeString("tgccccccccctgagaatgaatgtt ggacgaaata".replaceAll(" ", "")),
FastaUtils.asciiToRawQuality(
")*N!SV55!7@*`[4DRA8VKE-JF:KP0<D:/!K")); // tttgt aggtcggataaggcgttcgg atccgacacg
validator.setTemplate(
DnaUtils.encodeString("attgcccccctgagaatgaatgttatgtacggacgaaatatgtaaccata"));
validator.parse();
assertTrue(validator.getInvalidReason(), validator.isValid());
// second, non-rc
/*184100 131 simulatedSequence1 191 255 10=6N4=1X18= = 11 -180 AGCTTCTATAGCGGAATTGAGCGGAACCGCACG YTD$B1L!`_<"L'V8W=72T#YU]K@,#KUA> AS:i:1 NM:i:1 MQ:i:255 XU:Z:10=6N4=1X15=2B5= XQ:Z:%* XR:Z:A XA:i:1 IH:i:1
AGCTTCTATAGCGGAATTGAGCGGAACCGCGCACG
YTD$B1L!`_<"L'V8W=72T#YU]K@,%*#KUA>
*/
samrec.setAlignmentStart(2);
samrec.setCigarString("10=6N4=1X18=");
samrec.setReadString("AGCTTCTATAGCGGAATTGAGCGGAACCGCACG");
samrec.setBaseQualityString("YTD$B1L!`_<!L'V8W=72T#YU]K@,#KUA>");
samrec.setAttribute(SamUtils.CG_SUPER_CIGAR, "10=6N4=1X15=2B5=");
samrec.setAttribute(SamUtils.CG_OVERLAP_QUALITY, "%*");
samrec.setAttribute(SamUtils.CG_READ_DELTA, "A");
samrec.setFlags(131);
validator.setData(
samrec,
DnaUtils.encodeString("AGCTTCTATA GCGGAATTGAGCGGAACCGCGCACG".replaceAll(" ", "")),
FastaUtils.asciiToRawQuality(
"YTD$B1L!`_<!L'V8W=72T#YU]K@,%*#KUA>")); // YTD$B1L!`_ <!L'V8W=72T#YU]K@,%*#KUA>
validator.setTemplate(
DnaUtils.encodeString("TAGCTTCTATAGGGGGCGCGGTATTGAGCGGAACCGCACGTGCTATTTTCC"));
validator.parse();
assertTrue(validator.getInvalidReason(), validator.isValid());
// first, rc
/*137629 115 simulatedSequence1 195 255 10=6N9=1I13= = 13 -181 TCTATAGGGGTATTGAGCGAGAACCGCACGTGC ^#R"E\`,),UQANL6J/J"G/P'^;<RIX4O$ AS:i:2 NM:i:1 MQ:i:255 XU:Z:10=6N9=1I10=2B5= XQ:Z:<O XR:Z:A XA:i:3 IH:i:1
GCACGCGTGCGGTTCTCGCTCAATACCCCTATAGA
$O4XIO<R<;^'P/G"J/J6LNAQU,),`\E"R#^
*/
samrec.setAlignmentStart(6);
samrec.setCigarString("10=6N9=1I13=");
samrec.setReadString("TCTATAGGGGTATTGAGCGAGAACCGCACGTGC");
samrec.setBaseQualityString("^#R!E!`,),UQANL6J/J!G/P'^;<RIX4O$");
samrec.setAttribute(SamUtils.CG_SUPER_CIGAR, "10=6N9=1I10=2B5=");
samrec.setAttribute(SamUtils.CG_OVERLAP_QUALITY, "<O");
samrec.setAttribute(SamUtils.CG_READ_DELTA, "A");
samrec.setFlags(115);
validator.setData(
samrec,
DnaUtils.encodeString("GCACGCGTGCGGTTCTCGCTCAATA CCCCTATAGA".replaceAll(" ", "")),
FastaUtils.asciiToRawQuality(
"$O4XIO<R<;^'P/G!J/J6LNAQU,),`!E!R#^")); // YTD$B1L!`_ <!L'V8W=72T#YU]K@,%*#KUA>
validator.setTemplate(
DnaUtils.encodeString("TAGCTTCTATAGGGGGCGCGGTATTGAGCGGAACCGCACGTGCTATTTTCC"));
validator.parse();
assertTrue(validator.getInvalidReason(), validator.isValid());
// second, rc
/*137629 179 simulatedSequence1 13 255 9=1X13=6N10= = 195 181 AGAATGAATCTTATGTACGGACGGTAACCATAA ^#R"E,),UQANL6J/J"G/P'^;<R<OIX4O$ AS:i:1 NM:i:1 MQ:i:255 XU:Z:5=2B6=1X13=6N10= XQ:Z:\` XR:Z:C XA:i:3 IH:i:1
TTATGGTTACCGTCCGTACATAAGATTCATATTCT
$O4XIO<R<;^'P/G"J/J6LNAQU,),`\E"R#^
*/
samrec.setAlignmentStart(2);
samrec.setCigarString("9=1X13=6N10=");
samrec.setReadString("AGAATGAATCTTATGTACGGACGGTAACCATAA");
samrec.setBaseQualityString("^#R!E,),UQANL6J/J!G/P'^;<R<OIX4O$");
samrec.setAttribute(SamUtils.CG_SUPER_CIGAR, "5=2B6=1X13=6N10=");
samrec.setAttribute(SamUtils.CG_OVERLAP_QUALITY, "!`");
samrec.setAttribute(SamUtils.CG_READ_DELTA, "C");
samrec.setFlags(179);
validator.setData(
samrec,
DnaUtils.encodeString("TTATGGTTAC CGTCCGTACATAAGATTCATATTCT".replaceAll(" ", "")),
FastaUtils.asciiToRawQuality(
"$O4XIO<R<;^'P/G!J/J6LNAQU,),`!E!R#^")); // YTD$B1L!`_ <!L'V8W=72T#YU]K@,%*#KUA>
validator.setTemplate(DnaUtils.encodeString("GAGAATGAATGTTATGTACGGACGAAATATGTAACCATAACACC"));
validator.parse();
assertTrue(validator.getInvalidReason(), validator.isValid());
}
public void testSoftClip() throws Exception {
final SuperCigarValidator validator = new SuperCigarValidator(0);
final SAMRecord samrec = new SAMRecord(null);
samrec.setAlignmentStart(1);
samrec.setCigarString("3S2=18=5N9=1X");
samrec.setReadString("AGCCCACACGTAAATAAGACATCACGATGATCA");
samrec.setAttribute(SamUtils.CG_SUPER_CIGAR, "3S2=2B20=5N9=1X");
samrec.setBaseQualityString("4316%8883-56+141663,2.3----45/.,2");
samrec.setAttribute(SamUtils.CG_OVERLAP_QUALITY, "%6");
samrec.setAttribute(SamUtils.CG_READ_DELTA, "AGCA");
samrec.setAttribute(SamUtils.ATTRIBUTE_ALIGNMENT_SCORE, 4);
samrec.setFlags(67);
validator.setData(
samrec,
DnaUtils.encodeString("AGCCCCCACACGTAAATAAGACATC ACGATGATCA".replaceAll(" ", "")),
FastaUtils.asciiToRawQuality("4316%%68883-56+141663,2.3----45/.,2"));
validator.setTemplate(DnaUtils.encodeString("CCACACGTAAATAAGACATCGGGGGACGATGATCG"));
validator.parse();
assertTrue(validator.getInvalidReason(), validator.isValid());
// Alignment mismatch 3617884 153 chr18 1 255 4S19=7N2=1X7= * *
// * AAAACCCTAACCCTAACCCTAACCCCAACCCTA 998140-,7::;26;;.39'(2347-88989+7
// AS:i:2 NM:i:1 XU:Z:5=2B20=7N2=1X7= XR:Z:C XQ:Z:42 IH:i:1
samrec.setAlignmentStart(1);
samrec.setCigarString("4S19=7N2=1X7=");
samrec.setReadString("AAAACCCTAACCCTAACCCTAACCCCAACCCTA");
samrec.setAttribute(SamUtils.CG_SUPER_CIGAR, "4S1=2B1S19=7N2=1X7=");
samrec.setBaseQualityString("998140-,7::;26;;.39'(2347-88989+7");
samrec.setAttribute(SamUtils.CG_OVERLAP_QUALITY, "42");
samrec.setAttribute(SamUtils.CG_READ_DELTA, "AAAAAC");
samrec.setAttribute(SamUtils.ATTRIBUTE_ALIGNMENT_SCORE, 6);
samrec.setFlags(67);
validator.setData(
samrec,
DnaUtils.encodeString("AAAACACCCTAACCCTAACCCTAAC CCCAACCCTA".replaceAll(" ", "")),
FastaUtils.asciiToRawQuality("99814420-,7::;26;;.39'(2347-88989+7"));
validator.setTemplate(DnaUtils.encodeString("CCCTAACCCTAACCCTAACCCTTACCCCTAACCCTA"));
validator.parse();
assertTrue(validator.getInvalidReason(), validator.isValid());
// 153
// TAGGGTTGGG GTTAGGGTTAGGGTTAGGGTGTTTT"),
// DnaUtils.fastqToPhred("7+98988-7432('93.;;62;::7,-02441899"));
samrec.setAlignmentStart(1);
samrec.setCigarString("10=7N19=4S");
samrec.setReadString("AGCCCACACGTAAATAAGACATCACGATGATCA");
samrec.setAttribute(SamUtils.CG_SUPER_CIGAR, "10=7N19=1S2B1=4S");
samrec.setBaseQualityString("8:::::79:775986<=<<96576767679808");
samrec.setAttribute(SamUtils.CG_OVERLAP_QUALITY, "88");
samrec.setAttribute(SamUtils.CG_READ_DELTA, "AATCA");
samrec.setAttribute(SamUtils.ATTRIBUTE_ALIGNMENT_SCORE, 5);
samrec.setFlags(139);
validator.setData(
samrec,
DnaUtils.encodeString("AGCCCACACG TAAATAAGACATCACGATGAGATCA".replaceAll(" ", "")),
FastaUtils.asciiToRawQuality("8:::::79:775986<=<<9657676768879808"));
validator.setTemplate(DnaUtils.encodeString("AGCCCACACGTTCCCCTTAAATAAGACATCACGATG"));
validator.parse();
assertTrue(validator.getInvalidReason(), validator.isValid());
samrec.setFlags(115);
validator.setData(
samrec,
DnaUtils.encodeString("TGATCTCATCGTGATGTCTTATTTA CGTGTGGGCT".replaceAll(" ", "")),
FastaUtils.asciiToRawQuality("8089788676767569<<=<689577:97:::::8"));
validator.parse();
assertTrue(validator.getInvalidReason(), validator.isValid());
}