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added LOD threshold for determining when to clean 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@725 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-05-15 20:23:59 +00:00
parent 99d4ebc26d
commit f33f3c0434
1 changed files with 6 additions and 4 deletions
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10
java/src/org/broadinstitute/sting/playground/gatk/walkers/IntervalCleanerWalker.java
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@ -26,6 +26,8 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
public String OUT_INDELS = null; public String OUT_INDELS = null;
@Argument(fullName="OutputAllReads", shortName="all", doc="print out all reads (otherwise, just those within the intervals)", required=false) @Argument(fullName="OutputAllReads", shortName="all", doc="print out all reads (otherwise, just those within the intervals)", required=false)
public boolean printAllReads = false; public boolean printAllReads = false;
@Argument(fullName="LODThresholdForCleaning", shortName="LOD", doc="LOD threshold above which the cleaner will clean", required=false)
public double LOD_THRESHOLD = 5.0;
public static final int MAX_QUAL = 99; public static final int MAX_QUAL = 99;
@ -160,7 +162,7 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
StringBuffer sb = new StringBuffer(); StringBuffer sb = new StringBuffer();
sb.append(reference.substring(0, refIdx)); sb.append(reference.substring(0, refIdx));
Cigar c = swConsensus.getCigar(); Cigar c = swConsensus.getCigar();
//out.println("CIGAR = " + cigarToString(c)); logger.info("CIGAR = " + cigarToString(c));
int indelCount = 0; int indelCount = 0;
int altIdx = 0; int altIdx = 0;
@ -311,7 +313,7 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
// for reads that start in an insertion // for reads that start in an insertion
if ( !sawAlignmentStart && myPosOnAlt < endOfFirstBlock + altCE2.getLength() ) { if ( !sawAlignmentStart && myPosOnAlt < endOfFirstBlock + altCE2.getLength() ) {
aRead.getRead().setAlignmentStart(leftmostIndex + endOfFirstBlock); aRead.getRead().setAlignmentStart(leftmostIndex + endOfFirstBlock);
readCigar.add(new CigarElement(myPosOnAlt - endOfFirstBlock, CigarOperator.I)); readCigar.add(new CigarElement(altCE2.getLength() - (myPosOnAlt - endOfFirstBlock), CigarOperator.I));
indelOffsetOnRead = myPosOnAlt - endOfFirstBlock; indelOffsetOnRead = myPosOnAlt - endOfFirstBlock;
sawAlignmentStart = true; sawAlignmentStart = true;
} else if ( sawAlignmentStart ) { } else if ( sawAlignmentStart ) {
@ -582,7 +584,7 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
} }
// if the best alternate consensus has a smaller sum of quality score mismatches, then clean! // if the best alternate consensus has a smaller sum of quality score mismatches, then clean!
if ( bestConsensus != null && bestConsensus.mismatchSum < totalMismatchSum ) { if ( bestConsensus != null && ((double)(totalMismatchSum - bestConsensus.mismatchSum))/10.0 >= LOD_THRESHOLD ) {
logger.info("CLEAN: " + bestConsensus.str); logger.info("CLEAN: " + bestConsensus.str);
// clean the appropriate reads // clean the appropriate reads
@ -612,4 +614,4 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
} }
return b.toString(); return b.toString();
} }
} }