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fix(qsv): fixing issue where references didn't match #385

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Merged
merged 1 commit into from
Nov 26, 2024
Merged

fix(qsv): fixing issue where references didn't match #385

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28 changes: 20 additions & 8 deletions qsv/src/org/qcmg/qsv/splitread/SplitReadContig.java
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Original file line number Diff line number Diff line change
Expand Up @@ -219,6 +219,7 @@ public SplitReadAlignment getRight() {
}

public static SplitReadAlignment getSingleSplitReadAlignment(SplitReadAlignment left, SplitReadAlignment right) {

if (left == null && right != null) {
return right;
} else if (right == null && left != null) {
Expand Down Expand Up @@ -492,7 +493,7 @@ public void parseConsensusAlign(List<BLATRecord> records) throws QSVException, I
left = null;
right = null;

if (confidenceLevel.equals(QSVConstants.LEVEL_SINGLE_CLIP) || knownSV.equalReference()) {
if (confidenceLevel.equals(QSVConstants.LEVEL_SINGLE_CLIP) || knownSV.equalReference()) {
getSplitReadAlignments(null, records);
} else {
List<BLATRecord> leftRecords = new ArrayList<>();
Expand All @@ -506,12 +507,10 @@ public void parseConsensusAlign(List<BLATRecord> records) throws QSVException, I
rightRecords.add(r);
}
}
getTranslocationSplitReadAlignments(null, leftRecords, rightRecords);
getTranslocationSplitReadAlignments(null, leftRecords, rightRecords);
}



if (left != null & right != null) {
if (left != null & right != null & knownAndPotentialReferencesMatch(knownSV, left, right)) {

//rearrange
reorder();
Expand Down Expand Up @@ -609,6 +608,14 @@ public void parseConsensusAlign(List<BLATRecord> records) throws QSVException, I
}
}

public static boolean knownAndPotentialReferencesMatch(StructuralVariant currentSV, SplitReadAlignment leftAlign, SplitReadAlignment rightAlign) {
if (leftAlign != null & rightAlign != null) {
return (leftAlign.getReference().equals(currentSV.getLeftReference()) && rightAlign.getReference().equals(currentSV.getRightReference())) ||
(rightAlign.getReference().equals(currentSV.getLeftReference()) && leftAlign.getReference().equals(currentSV.getRightReference()));
}
return false;
}

public static boolean leftLower(int leftStart, int rightStart) {
return leftStart < rightStart;
}
Expand Down Expand Up @@ -652,7 +659,6 @@ void calculateMicrohomology() {
}

void recheckMicrohomologyForSingleAlignment() {

String leftRef = getReferenceSequence(splitreadSV.getLeftReference(), splitreadSV.getLeftBreakpoint() + 1, 0, 50, chromosomes);
String rightRef = getReferenceSequence(splitreadSV.getRightReference(), splitreadSV.getRightBreakpoint() - 1, 50, 0, chromosomes);
int end = leftSequence.length();
Expand Down Expand Up @@ -698,7 +704,11 @@ public static String getReferenceSequence(String reference, int breakpoint, int

ConcurrentMap<String,byte[]> referenceMap = QSVUtil.getReferenceMap();
byte[] basesArray = referenceMap.get(reference);


if (start > end) {
logger.info("In getReferenceSequence method - Reference: " + reference + "breakpoint: " + breakpoint + " chromosome: " + c.getName() + " chromosome length: " + c.getTotalLength() + " start: " + start + " end: " + end + " basesArray length: " + basesArray.length);
throw new IllegalArgumentException("Start of reference sequence to retrieve is greater than end: " + start + " " + end);
}
// array is zero-based, and picard is 1-based
return new String(Arrays.copyOfRange(basesArray, start - 1, end - 1));
}
Expand Down Expand Up @@ -937,7 +947,8 @@ private void getTranslocationSplitReadAlignments(SplitReadAlignment align, List<
}
if (index2 != -1) {
rightRecords.remove(index2);
}
}

getTranslocationSplitReadAlignments(getSingleSplitReadAlignment(left, right), leftRecords, rightRecords);
}
}
Expand Down Expand Up @@ -1101,4 +1112,5 @@ public static boolean matchingQueryString(int difference, int queryStart, int qu
public String getMutationType() {
return this.mutationType;
}

}
35 changes: 35 additions & 0 deletions qsv/test/org/qcmg/qsv/splitread/SplitReadContigTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -233,6 +233,41 @@ public void setSplitReadAlignments() {
assertEquals(true, right == null);
}

@Test
public void testknownAndPotentialReferencesMatch() {
StructuralVariant knownSV = new StructuralVariant("chr10", "chr10", 89700299, 89712341, "1");
SplitReadAlignment left = new SplitReadAlignment("chr10", QSVUtil.MINUS, 89700210, 89700299, 109, 282);
SplitReadAlignment right = new SplitReadAlignment("chr10", QSVUtil.MINUS, 89700210, 89700299, 109, 282);
assertTrue(SplitReadContig.knownAndPotentialReferencesMatch(knownSV, left, right));

knownSV = new StructuralVariant("chr10", "chr10", 89700299, 89712341, "1");
left = new SplitReadAlignment("chr12", QSVUtil.MINUS, 89700210, 89700299, 109, 282);
right = new SplitReadAlignment("chr10", QSVUtil.MINUS, 89700210, 89700299, 109, 282);
assertFalse(SplitReadContig.knownAndPotentialReferencesMatch(knownSV, left, right));

knownSV = new StructuralVariant("chr10", "chr10", 89700299, 89712341, "1");
left = new SplitReadAlignment("chr10", QSVUtil.MINUS, 89700210, 89700299, 109, 282);
right = new SplitReadAlignment("chr12", QSVUtil.MINUS, 89700210, 89700299, 109, 282);
assertFalse(SplitReadContig.knownAndPotentialReferencesMatch(knownSV, left, right));

knownSV = new StructuralVariant("chr10", "chr12", 89700299, 89712341, "1");
left = new SplitReadAlignment("chr12", QSVUtil.MINUS, 89700210, 89700299, 109, 282);
right = new SplitReadAlignment("chr10", QSVUtil.MINUS, 89700210, 89700299, 109, 282);
assertTrue(SplitReadContig.knownAndPotentialReferencesMatch(knownSV, left, right));

knownSV = new StructuralVariant("chr10", "chr12", 89700299, 89712341, "1");
left = new SplitReadAlignment("chr10", QSVUtil.MINUS, 89700210, 89700299, 109, 282);
right = new SplitReadAlignment("chr12", QSVUtil.MINUS, 89700210, 89700299, 109, 282);
assertTrue(SplitReadContig.knownAndPotentialReferencesMatch(knownSV, left, right));

knownSV = new StructuralVariant("chr10", "chr12", 89700299, 89712341, "1");
left = new SplitReadAlignment("chr10", QSVUtil.MINUS, 89700210, 89700299, 109, 282);
right = new SplitReadAlignment("chr10", QSVUtil.MINUS, 89700210, 89700299, 109, 282);
assertFalse(SplitReadContig.knownAndPotentialReferencesMatch(knownSV, left, right));


}

@Test
public void setSplitReadAlignments2() {
/*
Expand Down