From 8bc7afe7816214160fa11f553fbae7a461574da0 Mon Sep 17 00:00:00 2001 From: ebanks Date: Mon, 31 Aug 2009 04:29:19 +0000 Subject: [PATCH] Smarter SW penalties git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1488 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/indels/IntervalCleanerWalker.java | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalCleanerWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalCleanerWalker.java index 7407616bf..54e964bc4 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalCleanerWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalCleanerWalker.java @@ -45,6 +45,11 @@ public class IntervalCleanerWalker extends LocusWindowWalker // 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 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 statsOutput = null; private FileWriter snpsOutput = null; @@ -263,7 +268,7 @@ public class IntervalCleanerWalker extends LocusWindowWalker if ( altAlignmentsToTest.size() <= MAX_READS_FOR_CONSENSUSES ) { for ( AlignedRead aRead : altAlignmentsToTest ) { // 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()); if ( c != null) altConsenses.add(c); @@ -275,7 +280,7 @@ public class IntervalCleanerWalker extends LocusWindowWalker int index = generator.nextInt(altAlignmentsToTest.size()); AlignedRead aRead = altAlignmentsToTest.remove(index); // 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()); if ( c != null) altConsenses.add(c);