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Smarter SW penalties 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1488 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-08-31 04:29:19 +00:00
parent 463f80c03e
commit 8bc7afe781
1 changed files with 7 additions and 2 deletions
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9
java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalCleanerWalker.java
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@ -45,6 +45,11 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
// fraction of mismatches that need to no longer mismatch for a column to be considered cleaned // fraction of mismatches that need to no longer mismatch for a column to be considered cleaned
private static final double MISMATCH_COLUMN_CLEANED_FRACTION = 0.75; private static final double MISMATCH_COLUMN_CLEANED_FRACTION = 0.75;
private static final double SW_MATCH = 30.0; // 1.0;
private static final double SW_MISMATCH = -10.0; //-1.0/3.0;
private static final double SW_GAP = -10.0; //-1.0-1.0/3.0;
private static final double SW_GAP_EXTEND = -2.0; //-1.0/.0;
private FileWriter indelOutput = null; private FileWriter indelOutput = null;
private FileWriter statsOutput = null; private FileWriter statsOutput = null;
private FileWriter snpsOutput = null; private FileWriter snpsOutput = null;
@ -263,7 +268,7 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
if ( altAlignmentsToTest.size() <= MAX_READS_FOR_CONSENSUSES ) { if ( altAlignmentsToTest.size() <= MAX_READS_FOR_CONSENSUSES ) {
for ( AlignedRead aRead : altAlignmentsToTest ) { for ( AlignedRead aRead : altAlignmentsToTest ) {
// do a pairwise alignment against the reference // do a pairwise alignment against the reference
SWPairwiseAlignment swConsensus = new SWPairwiseAlignment(reference, aRead.getReadString()); SWPairwiseAlignment swConsensus = new SWPairwiseAlignment(reference, aRead.getReadString(), SW_MATCH, SW_MISMATCH, SW_GAP, SW_GAP_EXTEND);
Consensus c = createAlternateConsensus(swConsensus.getAlignmentStart2wrt1(), swConsensus.getCigar(), reference, aRead.getReadString()); Consensus c = createAlternateConsensus(swConsensus.getAlignmentStart2wrt1(), swConsensus.getCigar(), reference, aRead.getReadString());
if ( c != null) if ( c != null)
altConsenses.add(c); altConsenses.add(c);
@ -275,7 +280,7 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
int index = generator.nextInt(altAlignmentsToTest.size()); int index = generator.nextInt(altAlignmentsToTest.size());
AlignedRead aRead = altAlignmentsToTest.remove(index); AlignedRead aRead = altAlignmentsToTest.remove(index);
// do a pairwise alignment against the reference // do a pairwise alignment against the reference
SWPairwiseAlignment swConsensus = new SWPairwiseAlignment(reference, aRead.getReadString()); SWPairwiseAlignment swConsensus = new SWPairwiseAlignment(reference, aRead.getReadString(), SW_MATCH, SW_MISMATCH, SW_GAP, SW_GAP_EXTEND);
Consensus c = createAlternateConsensus(swConsensus.getAlignmentStart2wrt1(), swConsensus.getCigar(), reference, aRead.getReadString()); Consensus c = createAlternateConsensus(swConsensus.getAlignmentStart2wrt1(), swConsensus.getCigar(), reference, aRead.getReadString());
if ( c != null) if ( c != null)
altConsenses.add(c); altConsenses.add(c);