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Sync with Andrey's changes 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2723 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-01-28 20:49:38 +00:00
parent db429e1096
commit 6f11fe442a
1 changed files with 27 additions and 12 deletions
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39
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
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@ -565,8 +565,25 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
CigarElement altCE1 = altCigar.getCigarElement(0);
CigarElement altCE2 = altCigar.getCigarElement(1);
int leadingMatchingBlockLength = 0; // length of the leading M element or 0 if the leading element is I
CigarElement indelCE;
if ( altCE1.getOperator() == CigarOperator.I ) {
indelCE=altCE1;
if ( altCE2.getOperator() != CigarOperator.M )
throw new StingException("When first element of the alt consensus is I, the second one must be M. Actual: "+altCigar.toString());
}
else {
if ( altCE1.getOperator() != CigarOperator.M )
throw new StingException("First element of the alt consensus cigar must be M or I. Actual: "+altCigar.toString());
if ( altCE2.getOperator() == CigarOperator.I || altCE2.getOperator() == CigarOperator.D ) indelCE=altCE2;
else
throw new StingException("When first element of the alt consensus is M, the second one must be I or D. Actual: "+altCigar.toString());
leadingMatchingBlockLength = altCE1.getLength();
}
// the easiest thing to do is to take each case separately
int endOfFirstBlock = altPosOnRef + altCE1.getLength();
int endOfFirstBlock = altPosOnRef + leadingMatchingBlockLength;
boolean sawAlignmentStart = false;
// for reads starting before the indel
@ -585,30 +602,28 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
int indelOffsetOnRef = 0, indelOffsetOnRead = 0;
// forward along the indel
if ( altCE2.getOperator() == CigarOperator.I ) {
if ( indelCE.getOperator() == CigarOperator.I ) {
// for reads that end in an insertion
if ( myPosOnAlt + aRead.getReadLength() < endOfFirstBlock + altCE2.getLength() ) {
if ( myPosOnAlt + aRead.getReadLength() < endOfFirstBlock + indelCE.getLength() ) {
readCigar.add(new CigarElement(myPosOnAlt + aRead.getReadLength() - endOfFirstBlock, CigarOperator.I));
aRead.setCigar(readCigar);
return;
}
// for reads that start in an insertion
if ( !sawAlignmentStart && myPosOnAlt < endOfFirstBlock + altCE2.getLength() ) {
if ( !sawAlignmentStart && myPosOnAlt < endOfFirstBlock + indelCE.getLength() ) {
aRead.setAlignmentStart(leftmostIndex + endOfFirstBlock);
readCigar.add(new CigarElement(altCE2.getLength() - (myPosOnAlt - endOfFirstBlock), CigarOperator.I));
readCigar.add(new CigarElement(indelCE.getLength() - (myPosOnAlt - endOfFirstBlock), CigarOperator.I));
indelOffsetOnRead = myPosOnAlt - endOfFirstBlock;
sawAlignmentStart = true;
} else if ( sawAlignmentStart ) {
readCigar.add(altCE2);
indelOffsetOnRead = altCE2.getLength();
readCigar.add(indelCE);
indelOffsetOnRead = indelCE.getLength();
}
} else if ( altCE2.getOperator() == CigarOperator.D ) {
} else if ( indelCE.getOperator() == CigarOperator.D ) {
if ( sawAlignmentStart )
readCigar.add(altCE2);
indelOffsetOnRef = altCE2.getLength();
} else {
throw new RuntimeException("Operator of middle block is not I or D: " + altCE2.getOperator());
readCigar.add(indelCE);
indelOffsetOnRef = indelCE.getLength();
}
// for reads that start after the indel