zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

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
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

39
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
View File

@ -565,8 +565,25 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
CigarElement altCE1 = altCigar.getCigarElement(0); CigarElement altCE1 = altCigar.getCigarElement(0);
CigarElement altCE2 = altCigar.getCigarElement(1); 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 // the easiest thing to do is to take each case separately
int endOfFirstBlock = altPosOnRef + altCE1.getLength(); int endOfFirstBlock = altPosOnRef + leadingMatchingBlockLength;
boolean sawAlignmentStart = false; boolean sawAlignmentStart = false;
// for reads starting before the indel // for reads starting before the indel
@ -585,30 +602,28 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
int indelOffsetOnRef = 0, indelOffsetOnRead = 0; int indelOffsetOnRef = 0, indelOffsetOnRead = 0;
// forward along the indel // forward along the indel
if ( altCE2.getOperator() == CigarOperator.I ) { if ( indelCE.getOperator() == CigarOperator.I ) {
// for reads that end in an insertion // 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)); readCigar.add(new CigarElement(myPosOnAlt + aRead.getReadLength() - endOfFirstBlock, CigarOperator.I));
aRead.setCigar(readCigar); aRead.setCigar(readCigar);
return; return;
} }
// for reads that start in an insertion // for reads that start in an insertion
if ( !sawAlignmentStart && myPosOnAlt < endOfFirstBlock + altCE2.getLength() ) { if ( !sawAlignmentStart && myPosOnAlt < endOfFirstBlock + indelCE.getLength() ) {
aRead.setAlignmentStart(leftmostIndex + endOfFirstBlock); 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; indelOffsetOnRead = myPosOnAlt - endOfFirstBlock;
sawAlignmentStart = true; sawAlignmentStart = true;
} else if ( sawAlignmentStart ) { } else if ( sawAlignmentStart ) {
readCigar.add(altCE2); readCigar.add(indelCE);
indelOffsetOnRead = altCE2.getLength(); indelOffsetOnRead = indelCE.getLength();
} }
} else if ( altCE2.getOperator() == CigarOperator.D ) { } else if ( indelCE.getOperator() == CigarOperator.D ) {
if ( sawAlignmentStart ) if ( sawAlignmentStart )
readCigar.add(altCE2); readCigar.add(indelCE);
indelOffsetOnRef = altCE2.getLength(); indelOffsetOnRef = indelCE.getLength();
} else {
throw new RuntimeException("Operator of middle block is not I or D: " + altCE2.getOperator());
} }
// for reads that start after the indel // for reads that start after the indel