From 0e627bce93d475959bc8810d17d23d4745dd36da Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Fri, 12 Apr 2013 12:42:47 -0400 Subject: [PATCH] Slight update to Path SW parameters. -- Decreasing the match value means that we no longer think that ACTG vs. ATCG is best modeled by 1M1D1M1I1M, since we don't get so much value for the middle C match that we can pay two gap open penalties to get it. --- .../sting/gatk/walkers/haplotypecaller/graphs/Path.java | 2 +- .../walkers/haplotypecaller/graphs/KBestPathsUnitTest.java | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/Path.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/Path.java index 9d2d680c9..f232a4ce0 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/Path.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/Path.java @@ -86,7 +86,7 @@ public class Path { // used in the bubble state machine to apply Smith-Waterman to the bubble sequence // these values were chosen via optimization against the NA12878 knowledge base - public static final Parameters NEW_SW_PARAMETERS = new Parameters(20.0, -20.0, -26.0, -0.1); + public static final Parameters NEW_SW_PARAMETERS = new Parameters(10, -20.0, -26.0, -0.1); private static final byte[] STARTING_SW_ANCHOR_BYTES = "XXXXXXXXX".getBytes(); diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/KBestPathsUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/KBestPathsUnitTest.java index 90fdf1fa4..302866b55 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/KBestPathsUnitTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/KBestPathsUnitTest.java @@ -445,6 +445,7 @@ public class KBestPathsUnitTest extends BaseTest { Arrays.asList("", "C", "1I"), Arrays.asList("AAA", "CGT", "3D3I"), Arrays.asList("TAT", "CAC", "3M"), + Arrays.asList("GCTG", "GTCG", "4M"), Arrays.asList("AAAAA", "", "5D"), Arrays.asList("", "AAAAA", "5I"), Arrays.asList("AAAAACC", "CCGGGGGG", "5D2M6I") @@ -460,7 +461,7 @@ public class KBestPathsUnitTest extends BaseTest { return tests.toArray(new Object[][]{}); } - @Test(dataProvider = "SystematicRefAltSWTestData", enabled = true) + @Test(dataProvider = "SystematicRefAltSWTestData", enabled = !DEBUG) public void testRefAltSW(final String prefix, final String end, final String refMid, final String altMid, final String midCigar) { // Construct the assembly graph SeqGraph graph = new SeqGraph();