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use better entropy threshold and don't print out "new" SNPs (since they're just an antrifact of the low (arbitrary) threshold 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1070 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-06-22 15:30:08 +00:00
parent bcb64d92e9
commit 9e25229014
1 changed files with 5 additions and 5 deletions
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10
java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IntervalCleanerWalker.java
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@ -32,7 +32,7 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
@Argument(fullName="LODThresholdForCleaning", shortName="LOD", doc="LOD threshold above which the cleaner will clean", required=false)
public double LOD_THRESHOLD = 5.0;
@Argument(fullName="EntropyThreshold", shortName="entropy", doc="percentage of mismatches at a locus to be considered having high entropy", required=false)
public double MISMATCH_THRESHOLD = 0.25;
public double MISMATCH_THRESHOLD = 0.15;
@Argument(fullName="maxConsensuses", shortName="maxConsensuses", doc="max alternate consensuses to try (necesary to improve performance in deep coverage)", required=false)
public int MAX_CONSENSUSES = 30;
@Argument(fullName="maxReadsForConsensuses", shortName="greedy", doc="max reads used for finding the alternate consensuses (necesary to improve performance in deep coverage)", required=false)
@ -607,10 +607,10 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
sb.append(" SAME_SNP\n");
else
sb.append(" NOT_SNP\n");
} else if ( cleanedMismatchBases[i] > totalBases[i] * MISMATCH_THRESHOLD ) {
sb.append(reads.get(0).getRead().getReferenceName() + ":");
sb.append(((int)leftmostIndex + i));
sb.append(" NEW_SNP\n");
//} else if ( cleanedMismatchBases[i] > totalBases[i] * MISMATCH_THRESHOLD ) {
// sb.append(reads.get(0).getRead().getReferenceName() + ":");
// sb.append(((int)leftmostIndex + i));
// sb.append(" NEW_SNP\n");
}
}
}