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 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 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());
}
public void testBad() {
Diagnostic.setLogStream();
final SAMRecord rec = new SAMRecord(new SAMFileHeader());
rec.setReadString("TATTAGGATTGAGACTGGTAAAATGGNCCACCAAG");
rec.setBaseQualityString("/725361840-525251.68,0,.52!222254/2");
final VariantParams params = VariantParams.builder().create();
try {
new AlignmentEnvironmentCG(
new VariantAlignmentRecord(rec),
params,
MachineErrorParams.builder().machine(MachineType.COMPLETE_GENOMICS).create(),
null);
fail();
} catch (final NoTalkbackSlimException e) {
assertTrue(e.getMessage(), e.getMessage().startsWith("Invalid CG alignment."));
}
}
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 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.
}
public void test() {
final SAMRecord rec = new SAMRecord(new SAMFileHeader());
rec.setReadString("TATTAGGATTGAGACTGGTAAAATGGNCCACCAAG");
rec.setBaseQualityString("/725361840-525251.68,0,.52!222254/2");
rec.setReadPairedFlag(true);
final VariantParams params = VariantParams.builder().create();
final AbstractMachineErrorParams me =
MachineErrorParams.builder().machine(MachineType.COMPLETE_GENOMICS).create();
final AlignmentEnvironment se =
new AlignmentEnvironmentCG(new VariantAlignmentRecord(rec), params, me, null);
assertFalse(!se.isInverted());
final String exp =
""
+ "AlignmentEnvironment read=GAACCACCNGGTAAAATGGTCAGAGTTAGGATTAT "
+ "quality=["
+ "0.0200, 0.0398, 0.0126, 0.0100, 0.0200, 0.0200, 0.0200, 0.0200, 1.0000, 0.0200, "
+ "0.0100, 0.0501, 0.0794, 0.0316, 0.0794, 0.0050, 0.0079, 0.0501, 0.0251, 0.0100, "
+ "0.0200, 0.0100, 0.0200, 0.0100, 0.0631, 0.0316, 0.0126, 0.0050, 0.0251, 0.0079, "
+ "0.0158, 0.0100, 0.0200, 0.0063, 0.0398"
+ "] start=-1";
assertEquals(exp, se.toString());
}
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());
}
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 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 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());
}
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"));
}