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Got rid of annoying commented printouts; no functional changes 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2881 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2010-02-24 05:12:30 +00:00
parent d73bc490c2
commit 27d3ef9458
1 changed files with 4 additions and 33 deletions
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37
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
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@ -74,7 +74,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
@Argument(fullName="writerWindowSize", shortName="writerWindowSize", doc="the window over which the writer will store reads when --sortInMemory is enabled", required=false)
protected int SORTING_WRITER_WINDOW = 100;
// the intervals input by the user
private Iterator<GenomeLoc> intervals = null;
@ -108,8 +108,6 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
private FileWriter statsOutput = null;
private FileWriter snpsOutput = null;
// private boolean DEBUG = true;
public void initialize() {
if ( LOD_THRESHOLD < 0.0 )
@ -411,17 +409,13 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
final AlignedRead aRead = new AlignedRead(read);
// if ( DEBUG ) System.out.println("\nREAD "+read.getReadName());
// first, move existing indels (for 1 indel reads only) to leftmost position within identical sequence
int numBlocks = AlignmentUtils.getNumAlignmentBlocks(read);
if ( numBlocks == 2 ) {
// if ( DEBUG ) System.out.println("Attempting to left-shift: read "+read.getReadName()+" alignment: "+read.getCigar().toString()+
// " at "+read.getAlignmentStart()+"; ref chunk starts at "+leftmostIndex);
Cigar newCigar = indelRealignment(read.getCigar(), reference, read.getReadBases(), read.getAlignmentStart()-(int)leftmostIndex, 0);
if ( aRead.setCigar(newCigar) ) {
// if ( DEBUG ) System.out.println("CIGAR CHANGED to "+newCigar.toString()) ;
leftMovedIndels.add(aRead);
}
}
@ -439,10 +433,9 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
if ( numBlocks == 2 ) {
Consensus c = createAlternateConsensus(aRead.getAlignmentStart() - (int)leftmostIndex, aRead.getCigar(), reference, aRead.getRead().getReadBases());
if ( c == null ) {} //System.out.println("ERROR: Failed to create alt consensus for read "+aRead.getRead().getReadName());
else {
// if ( DEBUG ) System.out.println("Adding consensus: read start "+aRead.getAlignmentStart()+" ref offset "+leftmostIndex+" read cigar "+aRead.getCigar());
else
altConsenses.add(c);
}
}
else {
// if ( debugOn ) System.out.println("Going to test...");
@ -464,7 +457,6 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
Consensus c = createAlternateConsensus(swConsensus.getAlignmentStart2wrt1(), swConsensus.getCigar(), reference, aRead.getRead().getReadBases());
if ( c != null ) {
// if ( debugOn ) System.out.println("NEW consensus generated by SW: "+c.str ) ;
// if ( DEBUG ) System.out.println("Found SW consensus: ref starts at "+leftmostIndex+" alignment at "+swConsensus.getAlignmentStart2wrt1()+" cigar "+swConsensus.getCigar().toString());
altConsenses.add(c);
} else {
// if ( debugOn ) System.out.println("FAILED to create Alt consensus from SW");
@ -511,16 +503,6 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
// the mismatch score is the min of its alignment vs. the reference and vs. the alternate
int myScore = altAlignment.second;
// if ( DEBUG ) {
// if ( toTest.getRead().getReadName().equals("302U3AAXX090430:1:35:429:1940#0") ) {
// System.out.println("READ: new score="+myScore+"; old score="+toTest.getMismatchScoreToReference() );
// }
// if ( toTest.getRead().getReadName().equals("426RRAAXX090524:8:42:1730:53#0") ) {
// System.out.println("READ: new score="+myScore+"; old score="+toTest.getMismatchScoreToReference() +" start at "+toTest.getAlignmentStart());
// }
// System.out.println(toTest.getRead().getReadName()+" old score="+toTest.getMismatchScoreToReference()+" new score="+myScore );
//
// }
if ( myScore >= toTest.getMismatchScoreToReference() )
myScore = toTest.getMismatchScoreToReference();
// keep track of reads that align better to the alternate consensus.
@ -538,15 +520,12 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
break;
}
// if ( DEBUG ) System.out.println("Consensus score: "+consensus.mismatchSum);
//logger.debug(consensus.str + " " + consensus.mismatchSum);
if ( bestConsensus == null || bestConsensus.mismatchSum > consensus.mismatchSum) {
// we do not need this alt consensus, release memory right away!!
if ( bestConsensus != null )
bestConsensus.readIndexes.clear();
bestConsensus = consensus;
// if ( DEBUG ) System.out.println("Current consensus is better!");
//logger.debug(consensus.str + " " + consensus.mismatchSum);
} else {
// we do not need this alt consensus, release memory right away!!
@ -1009,8 +988,6 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
// for now, we'll just punt the issue and not try to realign these
return cigar;
// if ( DEBUG ) System.out.println("Indel sequence: "+new String(indelString));
// now we have to check all WHOLE periods of the indel sequence:
// for instance, if
// REF: AGCTATATATAGCC
@ -1030,13 +1007,11 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
// position, we will move insertion left, to the position right after CA. This way, while moving the indel across the repeat
// on the ref, we can theoretically move it across a non-repeat on the read if the latter has a mismtach.
// if ( DEBUG ) System.out.println("Starting with "+indelIndexOnRef+" on the ref");
while ( period < indel_length ) { // we will always get at least trivial period = indelStringLength
period = BaseUtils.sequencePeriod(indelString, period+1);
if ( indel_length % period != 0 ) continue; // if indel sequence length is not a multiple of the period, it's not gonna work
// if ( DEBUG ) System.out.println("Checking period of "+period);
int newIndex = indelIndexOnRef;
@ -1055,11 +1030,9 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
}
}
if ( match ) {
// if ( DEBUG ) System.out.println("Success! Moving left by "+period);
newIndex -= period; // yes, they are the same, we can move indel farther left by at least period bases, go check if we can do more...
}
else {
// if ( DEBUG ) System.out.println("Can not push further left with period "+period+"; adjusted position: "+newIndex);
break; // oops, no match, can not push indel farther left
}
}
@ -1077,8 +1050,6 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
if ( difference > 0 ) {
// if ( DEBUG ) System.out.println("Best offset found: "+difference);
// The following if() statement: this should've never happened, unless the alignment is really screwed up.
// A real life example:
//