public void testCompare() {
final AlignmentResult ar1 = new AlignmentResult(new byte[0], new int[3], new byte[0]);
ar1.setIdentifyingInfo(false, true);
ar1.setRemainingOutput(-2, 0);
final AlignmentResult ar2 = new AlignmentResult(new byte[0], new int[3], new byte[0]);
ar2.setIdentifyingInfo(false, true);
ar2.setRemainingOutput(-2, 0);
// assertEquals(0, ar1.compareTo(ar2));
assertTrue(ar1.equals(ar2));
ar2.setIdentifyingInfo(false, false);
// assertTrue(ar1.compareTo(ar2) > 0);
assertFalse(ar1.equals(ar2));
ar2.setIdentifyingInfo(false, true);
ar2.setRemainingOutput(-2, 1);
// assertTrue(ar1.compareTo(ar2) < 0);
assertFalse(ar1.equals(ar2));
final AlignmentResult ar3 =
new AlignmentResult(new byte[0], ActionsHelper.build("", 2, 3), new byte[0]);
ar3.setIdentifyingInfo(false, true);
ar3.setRemainingOutput(-2, 0);
// assertTrue(ar1.compareTo(ar3) < 0);
assertFalse(ar1.equals(ar3));
assertNotNull(ar1);
}
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));
}
}
private void runSAMPairedEnd(
AlignmentResult mate, int pos, String complement, String expected, boolean first)
throws Exception {
final AlignmentResult ar =
new AlignmentResult(
getSequence(SAM_SEQ),
ActionsHelper.build("==========NNNNN=========================", pos - 1, 1),
getSequence(SAM_SEQ + "aaaaaaa"));
ar.setIdentifyingInfo(first, complement.equals("R"));
ar.mReferenceId = 7;
final File f = File.createTempFile("junit", "sam");
try {
final BinaryTempFileRecord sam = ar.toRecord(mate != null, mate, 0, false, false);
final String x = bcarToSamString(sam).replace('\t', '#');
assertEquals(x, expected, x);
assertEquals(complement.equals("R"), sam.isReverseStrand());
assertEquals((sam.getSamFlags() & SamBamConstants.SAM_READ_IS_PAIRED) == 0, mate == null);
if (mate != null) {
assertTrue(sam.isReadPaired());
assertEquals(mate.getStart(), sam.getMatePosition() - 1);
assertEquals(first, sam.isFirstOfPair());
assertEquals(!first, sam.isSecondOfPair());
} else {
assertFalse(sam.isReadPaired());
assertEquals(0, sam.getMatePosition());
assertFalse(sam.isFirstOfPair());
assertFalse(sam.isSecondOfPair());
}
} finally {
assertTrue(f.delete());
}
}
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 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 testBug867() {
final AlignmentResult ar =
new AlignmentResult(
getSequence("taaataatggcaatatctgcaggga aaactataag"),
ActionsHelper.build("", 0, 0),
getSequence("taa...atggcaatatctgcagggaacaggaaactataag"));
assertEquals(0, ar.mismatches());
}
public void testSAMPEDeletion() throws Exception {
final AlignmentResult mate =
new AlignmentResult(
getSequence("ACGT"), ActionsHelper.build("", 12, 2), getSequence("AC-T"));
mate.mReferenceId = 7;
mate.setIdentifyingInfo(false, true);
runSAMPairedEnd(mate, 1, "F", "0#163#7#1#*#10=5N25=#=#13#40#*#*#AS:i:1#NM:i:0", false);
}
private void runSAM(final String complement, final String expected) throws Exception {
runSAMPairedEnd(
new AlignmentResult(null, ActionsHelper.build("", 0, 0), null),
1,
complement,
expected,
false);
}
public void testSAMPESoftLeftClip() throws Exception {
final AlignmentResult mate =
new AlignmentResult(
getSequence("ACGT"), ActionsHelper.build("", 12, 2), getSequence(SAM_SEQ));
mate.mReferenceId = 0;
mate.setIdentifyingInfo(false, true);
// SAI: The ISIZE below may be wrong if we are supposed to use the inferred start of 1
runSAMPairedEnd(mate, -2, "F", "0#163#7#1#*#3S7=5N25=#=#13#40#*#*#AS:i:1#NM:i:0", false);
}
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 testCGAttrNew() {
final byte[] qualityScores = new byte[35];
for (int i = 0; i < qualityScores.length; i++) {
qualityScores[i] = (byte) i;
}
String read, acts, tmpl;
AlignmentResult ar;
BinaryTempFileRecord sr;
// First arm, !rc
read = "tcatg a ggcacatcg gcattacagc cagactgtcg";
acts = "=====BBB=D=X======= ========== NNNN ==========".replaceAll(" ", "");
tmpl = "tcatg acacatcg gcattacagc aggc cagactgtcg";
ar = new AlignmentResult(getSequence(read), ActionsHelper.build(acts, 0, 0), getSequence(tmpl));
ar.setIdentifyingInfo(true, false);
ar.setRemainingOutput(1, 0);
//
// assertEquals("tcatggcacatcggcattacagc....cagactgtcg\ttcatgacacatcggcattacagcaggccagactgtcg\t||||| ||||||||||||||||| ||||||||||", ar.tabularString());
sr = ar.toRecord(true, null, 0, false, false);
assertEquals("5=1X17=4N10=", new String(sr.getCigarString()));
assertEquals("5=3B1=1D1=1X17=4N10=", new String(sr.getSuperCigarString()));
assertEquals("G", new String(sr.getReadDeltaString()));
assertEquals("TCATGGCACATCGGCATTACAGCCAGACTGTCG", new String(sr.getCgReadString()));
assertEquals(33, sr.getCgReadString().length);
// first arm, !rc again, but with no errors.
read = "tcatg atgcacatcg gcattacagc cagactgtcg";
acts = "=====BBB========== ========== NNNN ==========".replaceAll(" ", "");
tmpl = "tcatg cacatcg gcattacagc aggc cagactgtcg";
ar = new AlignmentResult(getSequence(read), ActionsHelper.build(acts, 0, 0), getSequence(tmpl));
ar.setIdentifyingInfo(true, false);
ar.setRemainingOutput(1, 0);
sr = ar.toRecord(true, null, 0, false, false);
assertEquals("22=4N10=", new String(sr.getCigarString()));
assertEquals("5=3B20=4N10=", new String(sr.getSuperCigarString()));
assertEquals(0, sr.getReadDeltaString().length);
assertEquals("TCATGCACATCGGCATTACAGCCAGACTGTCG", new String(sr.getCgReadString()));
// First arm, rc
read = "tattt ttcgaggact tattttaatt ctcaaacgcg";
// tmprc tattt ggact tattttaatt aattg ctcaaacgct
acts = "=====BBB==IIX===== ========== NNNNN =========X".replaceAll(" ", "");
tmpl =
"agcgtttgag caatt aattaaaata agtcc aaata agagagagagagaga"; // is reverse complement
// compared to the read
ar = new AlignmentResult(getSequence(read), ActionsHelper.build(acts, 0, 0), getSequence(tmpl));
// ====D=================================== ====D===================================
ar.setIdentifyingInfo(true, true);
ar.setRemainingOutput(1, 0);
//
// assertEquals("tatttggacttattttaatt.....ctcaaacgcg\ttatttggacttattttaattaattgctcaaacgct\t|||||||||||||||||||| ||||||||| ", ar.tabularString());
assertEquals("TATTT" + "GGACT" + "TATTTTAATT" + "CTCAAACGCG", ar.readString());
sr = ar.toRecord(true, null, 0, false, false);
assertEquals("1X9=5N20=", new String(sr.getCigarString()));
assertEquals("1X9=5N15=1X2I2=3B5=", new String(sr.getSuperCigarString()));
assertEquals("CTCG", new String(sr.getReadDeltaString()));
assertEquals("CGCGTTTGAGAATTAAAATAAGTCCAAATA", new String(sr.getCgReadString()));
assertEquals(30, sr.getCgReadString().length);
// second arm, rc
read = "ctgctgaccc gacctactgg cggactcgag agtta";
acts = "========== NNNNNNNN ========== ========X=BBX====".replaceAll(" ", "");
tmpl = "ctgctgaccc agagccgg gacctactgg cggactcg ggtta";
ar = new AlignmentResult(getSequence(read), ActionsHelper.build(acts, 0, 0), getSequence(tmpl));
ar.setIdentifyingInfo(false, true);
ar.setRemainingOutput(1, 0);
sr = ar.toRecord(true, null, 0, false, false);
assertEquals("4=1X18=8N10=", new String(sr.getCigarString()));
assertEquals("4=1X2B1=1X18=8N10=", new String(sr.getSuperCigarString()));
assertEquals("TT", new String(sr.getReadDeltaString()));
assertEquals("TAACTCGAGTCCGCCAGTAGGTCGGGTCAGCAG", new String(sr.getCgReadString()));
assertEquals(33, sr.getCgReadString().length);
// second arm, !rc
read = "ttccggtctt ctctctatcc cgctggtttt acagg";
acts = "========== NNNNNNN ========== ========XXBB=I===".replaceAll(" ", "");
tmpl = "ttccggtctt tgtcttt ctctctatcc cgctggtt a agg attatatatat";
ar = new AlignmentResult(getSequence(read), ActionsHelper.build(acts, 0, 0), getSequence(tmpl));
ar.setIdentifyingInfo(false, false);
ar.setRemainingOutput(1, 0);
sr = ar.toRecord(true, null, 0, false, false);
assertEquals("10=7N19=1I3=", new String(sr.getCigarString()));
assertEquals("10=7N18=2X2B1=1I3=", new String(sr.getSuperCigarString()));
assertEquals("TTC", new String(sr.getReadDeltaString()));
assertEquals("TTCCGGTCTTCTCTCTATCCCGCTGGTTACAGG", new String(sr.getCgReadString()));
assertEquals(33, sr.getCgReadString().length);
// second arm, !rc (again, but with the whole overlap counteracted by insertions)
read = "ttccggtctt ctctctatcc cgctggtttt atagg";
acts = "========== NNNNNNN ========== ==========DDBB=I===".replaceAll(" ", "");
tmpl =
"ttccggtctt tgtcttt ctctctatcc cgctggtttt a agg atatatatat";
ar = new AlignmentResult(getSequence(read), ActionsHelper.build(acts, 0, 0), getSequence(tmpl));
ar.setIdentifyingInfo(false, false);
ar.setRemainingOutput(1, 0);
sr = ar.toRecord(true, null, 5, false, false);
assertEquals("10=7N21=1I3=", new String(sr.getCigarString()));
assertNotNull(sr.getSuperCigarString());
assertEquals("10=7N20=2D2B1=1I3=", new String(sr.getSuperCigarString()));
assertNotNull(sr.getReadDeltaString());
assertEquals("T", new String(sr.getReadDeltaString()));
assertEquals("TTCCGGTCTTCTCTCTATCCCGCTGGTTTTATAGG", new String(sr.getCgReadString()));
assertEquals(35, sr.getCgReadString().length);
assertEquals(6, sr.getStartPosition());
}
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());
}
