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 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 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 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 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());
}
/**
* HACK TO CREATE GATKSAMRECORD BASED ONLY A SAMRECORD FOR TESTING PURPOSES ONLY
*
* @param read
*/
public GATKSAMRecord(final SAMRecord read) {
super(read.getHeader());
super.setReferenceIndex(read.getReferenceIndex());
super.setAlignmentStart(read.getAlignmentStart());
super.setReadName(read.getReadName());
super.setMappingQuality(read.getMappingQuality());
// indexing bin done below
super.setCigar(read.getCigar());
super.setFlags(read.getFlags());
super.setMateReferenceIndex(read.getMateReferenceIndex());
super.setMateAlignmentStart(read.getMateAlignmentStart());
super.setInferredInsertSize(read.getInferredInsertSize());
SAMReadGroupRecord samRG = read.getReadGroup();
SAMBinaryTagAndValue samAttr = GATKBin.getReadBinaryAttributes(read);
if (samAttr == null) {
clearAttributes();
} else {
setAttributes(samAttr);
}
if (samRG != null) {
GATKSAMReadGroupRecord rg = new GATKSAMReadGroupRecord(samRG);
setReadGroup(rg);
}
super.setFileSource(read.getFileSource());
super.setReadName(read.getReadName());
super.setCigarString(read.getCigarString());
super.setReadBases(read.getReadBases());
super.setBaseQualities(read.getBaseQualities());
// From SAMRecord constructor: Do this after the above because setCigarString will clear it.
GATKBin.setReadIndexingBin(this, GATKBin.getReadIndexingBin(read));
}
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 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"));
}
@Override
public void execute() {
log.info("Initializing kmer code map...");
Map<Character, Integer> kmerCodeIndices = new HashMap<Character, Integer>();
kmerCodeIndices.put('0', 1);
kmerCodeIndices.put('A', 3);
kmerCodeIndices.put('B', 4);
kmerCodeIndices.put('C', 5);
kmerCodeIndices.put('_', 6);
kmerCodeIndices.put('.', 7);
kmerCodeIndices.put('1', 9);
Map<Character, String> kmerCodeNames = new LinkedHashMap<Character, String>();
kmerCodeNames.put('0', "ref0");
kmerCodeNames.put('A', "repetitive");
kmerCodeNames.put('B', "both");
kmerCodeNames.put('C', "lowcoverage");
kmerCodeNames.put('_', "lowconfidence");
kmerCodeNames.put('.', "novel");
kmerCodeNames.put('1', "ref1");
if (KMER_CODE_NAMES != null) {
for (Character c : kmerCodeNames.keySet()) {
String cStr = String.valueOf(c);
if (KMER_CODE_NAMES.containsKey(cStr)) {
kmerCodeNames.put(c, KMER_CODE_NAMES.get(cStr));
}
}
}
for (Character c : kmerCodeNames.keySet()) {
log.info(" {} {}: {}", c, kmerCodeIndices.get(c), kmerCodeNames.get(c));
}
log.info("Loading annotated contigs...");
Map<String, Map<String, String>> annotatedContigs = new HashMap<String, Map<String, String>>();
int kmerSize = 0;
if (ANN.length() > 0) {
TableReader tr = new TableReader(ANN);
for (Map<String, String> te : tr) {
String contigName = te.get("contigName");
if (kmerSize == 0) {
kmerSize = te.get("seq").length() - te.get("kmerOrigin").length() + 1;
}
annotatedContigs.put(contigName, te);
String[] ref0ToCanonicalExact =
(te.get("ref0ToCanonicalExact").equals("NA")
|| te.get("ref0ToCanonicalExact").equals("*:0-0")
? "NA:0-0"
: te.get("ref0ToCanonicalExact"))
.split("[:-]");
String[] ref1ToCanonicalExact =
(te.get("ref1ToCanonicalExact").equals("NA")
|| te.get("ref1ToCanonicalExact").equals("*:0-0")
? "NA:0-0"
: te.get("ref1ToCanonicalExact"))
.split("[:-]");
cout.println(
te.get("sampleName")
+ "_"
+ te.get("accession")
+ "_"
+ contigName
+ " "
+ ref0ToCanonicalExact[0]
+ " "
+ ref0ToCanonicalExact[1]
+ " "
+ ref0ToCanonicalExact[2]
+ " radius1=0.8r");
cout.println(
te.get("sampleName")
+ "_"
+ te.get("accession")
+ "_"
+ contigName
+ " "
+ ref1ToCanonicalExact[0]
+ " "
+ ref1ToCanonicalExact[1]
+ " "
+ ref1ToCanonicalExact[2]
+ " radius2=0.6r");
}
}
log.info(" contigs: {}", annotatedContigs.size());
log.info(" kmer size: {}", kmerSize);
log.info("Computing kmer inheritance information...");
SAMFileHeader sfh = CONTIGS.getFileHeader();
for (Character c : kmerCodeNames.keySet()) {
SAMReadGroupRecord rgr = new SAMReadGroupRecord(kmerCodeNames.get(c));
rgr.setSample(kmerCodeNames.get(c));
sfh.addReadGroup(rgr);
}
SAMFileWriterFactory sfwf = new SAMFileWriterFactory();
sfwf.setCreateIndex(true);
SAMFileWriter sfw = sfwf.makeBAMWriter(sfh, false, bout);
TableWriter tw = new TableWriter(sout);
Set<IGVEntry> igvEntries = new TreeSet<IGVEntry>();
int numContigs = 0;
for (SAMRecord contig : CONTIGS) {
if (CONTIG_NAMES == null
|| CONTIG_NAMES.isEmpty()
|| CONTIG_NAMES.contains(contig.getReadName())) {
Map<String, String> te = annotatedContigs.get(contig.getReadName());
if (annotatedContigs.containsKey(contig.getReadName())) {
String seq = contig.getReadString();
// log.debug(" te: {}", te);
String annSeq = te.get("seq");
String kmerOrigin = te.get("kmerOrigin");
Map<CortexKmer, Character> kmerCodes = new HashMap<CortexKmer, Character>();
for (int i = 0; i < kmerOrigin.length(); i++) {
CortexKmer kmer = new CortexKmer(annSeq.substring(i, i + kmerSize));
Character code = kmerOrigin.charAt(i);
kmerCodes.put(kmer, code);
}
Map<Character, Integer> kmerStats = new HashMap<Character, Integer>();
for (Character c : kmerCodeNames.keySet()) {
kmerStats.put(c, 0);
}
boolean changed = false;
// We want to be able to examine soft-clipped regions as well.
List<CigarElement> ces = new ArrayList<CigarElement>();
for (CigarElement ce : contig.getCigar().getCigarElements()) {
if (ce.getOperator().equals(CigarOperator.S)) {
ces.add(new CigarElement(ce.getLength(), CigarOperator.M));
changed = true;
} else {
ces.add(ce);
}
}
if (changed) {
CigarElement firstCe = contig.getCigar().getCigarElements().get(0);
if (firstCe.getOperator().equals(CigarOperator.S)) {
contig.setAlignmentStart(contig.getAlignmentStart() - firstCe.getLength());
}
contig.setCigar(new Cigar(ces));
}
for (AlignmentBlock ab : contig.getAlignmentBlocks()) {
for (int i = ab.getReadStart() - 1; i < ab.getReadStart() + ab.getLength(); i++) {
if (i + kmerSize < seq.length()) {
CortexKmer kmer = new CortexKmer(seq.substring(i, i + kmerSize));
SAMRecord skmer = new SAMRecord(CONTIGS.getFileHeader());
skmer.setReadBases(seq.substring(i, i + kmerSize).getBytes());
List<CigarElement> cigarElements = new ArrayList<CigarElement>();
cigarElements.add(new CigarElement(kmerSize, CigarOperator.M));
Cigar cigar = new Cigar(cigarElements);
skmer.setReadName(contig.getReadName() + "." + kmer.getKmerAsString());
skmer.setReferenceName(contig.getReferenceName());
skmer.setCigar(cigar);
skmer.setReadPairedFlag(false);
skmer.setDuplicateReadFlag(false);
skmer.setMateNegativeStrandFlag(false);
skmer.setAlignmentStart(ab.getReferenceStart() - ab.getReadStart() + 1 + i);
skmer.setAttribute("RG", "none");
skmer.setMappingQuality(0);
Character c = kmerCodes.get(kmer);
String codeName = kmerCodeNames.get(c);
String parentReadGroupId = null;
String sampleReadGroupId = null;
for (SAMReadGroupRecord rgr : sfh.getReadGroups()) {
if (rgr.getSample().equals(codeName)) {
parentReadGroupId = rgr.getReadGroupId();
}
if (rgr.getSample().equals(contig.getReadGroup().getSample())) {
sampleReadGroupId = rgr.getReadGroupId();
}
}
skmer.setAttribute(
"RG", parentReadGroupId != null ? parentReadGroupId : sampleReadGroupId);
skmer.setMappingQuality(99);
sfw.addAlignment(skmer);
kmerStats.put(c, kmerStats.get(c) + 1);
IGVEntry igvEntry = new IGVEntry();
igvEntry.chromosome = contig.getReferenceName();
igvEntry.start = ab.getReferenceStart() - ab.getReadStart() + i;
igvEntry.parentageName = kmerCodeNames.get(c);
igvEntry.parentage = kmerCodeIndices.get(c);
igvEntries.add(igvEntry);
}
}
}
if (!contig.isSecondaryOrSupplementary()) {
beout.println(
contig.getReferenceName()
+ "\t"
+ contig.getAlignmentStart()
+ "\t"
+ contig.getAlignmentEnd()
+ "\t"
+ contig.getReadName()
+ "."
+ contig.getReadGroup().getSample());
if (annotatedContigs.size() > 10 && numContigs % (annotatedContigs.size() / 10) == 0) {
log.info(" processed {}/{} contigs", numContigs, annotatedContigs.size());
}
numContigs++;
}
Map<String, String> stats = new LinkedHashMap<String, String>();
stats.put("contigName", contig.getReadName());
stats.put("sampleName", contig.getReadGroup().getSample());
for (Character c : kmerCodeNames.keySet()) {
stats.put(kmerCodeNames.get(c), String.valueOf(kmerStats.get(c)));
}
tw.addEntry(stats);
}
}
}
log.info("Writing kmer inheritance information...");
out.printf("%s\t%s\t%s\t%s\t%s\n", "Chromosome", "Start", "End", "Feature", "Parentage");
for (IGVEntry igvEntry : igvEntries) {
out.printf(
"%s\t%d\t%d\t%s\t%d\n",
igvEntry.chromosome,
igvEntry.start,
igvEntry.start + 1,
igvEntry.parentageName,
igvEntry.parentage);
}
sfw.close();
}
