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Fix bug in realigning insertion cigar strings 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@914 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-06-05 18:46:41 +00:00
parent 199be46c36
commit 4623a34ad3
2 changed files with 3 additions and 3 deletions
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4
java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IntervalCleanerWalker.java
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@ -529,7 +529,7 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
} }
logger.debug("Original mismatch columns = " + originalMismatchColumns + "; cleaned mismatch columns = " + cleanedMismatchColumns); logger.debug("Original mismatch columns = " + originalMismatchColumns + "; cleaned mismatch columns = " + cleanedMismatchColumns);
//out.println("Original mismatch columns = " + originalMismatchColumns + "; cleaned mismatch columns = " + cleanedMismatchColumns); //out.println("**** Original mismatch columns = " + originalMismatchColumns + "; cleaned mismatch columns = " + cleanedMismatchColumns);
return (originalMismatchColumns == 0 || cleanedMismatchColumns < originalMismatchColumns); return (originalMismatchColumns == 0 || cleanedMismatchColumns < originalMismatchColumns);
} }
@ -551,7 +551,7 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
} }
difference = indelIndex - newIndex; difference = indelIndex - newIndex;
} else if ( ce2.getOperator() == CigarOperator.I ) { } else if ( ce2.getOperator() == CigarOperator.I ) {
int indelIndex = ce1.getLength(); int indelIndex = refIndex + ce1.getLength();
String indelString = readSeq.substring(indelIndex, indelIndex+ce2.getLength()); String indelString = readSeq.substring(indelIndex, indelIndex+ce2.getLength());
int newIndex = indelIndex; int newIndex = indelIndex;
while ( newIndex > 0 ) { while ( newIndex > 0 ) {

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/MismatchIntervalWalker.java
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@ -16,7 +16,7 @@ public class MismatchIntervalWalker extends LocusWalker<Pair<GenomeLoc, Boolean>
@Argument(fullName="windowSize", shortName="window", doc="window size for calculating entropy", required=false) @Argument(fullName="windowSize", shortName="window", doc="window size for calculating entropy", required=false)
public int windowSize = 10; public int windowSize = 10;
@Argument(fullName="mismatchFraction", shortName="mismatch", doc="fraction of mismatching base qualities threshold", required=false) @Argument(fullName="mismatchFraction", shortName="mismatch", doc="fraction of mismatching base qualities threshold", required=false)
public double mismatchThreshold = 0.20; public double mismatchThreshold = 0.15;
private final int minReadsAtInterval = 4; private final int minReadsAtInterval = 4;