From 0e057276ae3758d2a48baad5d64b012cae0471b9 Mon Sep 17 00:00:00 2001 From: droazen Date: Wed, 22 Jun 2011 22:53:58 +0000 Subject: [PATCH] Changing the default behavior of the IndelRealigner to run without Smith-Waterman. Changed around the integration tests accordingly. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6039 348d0f76-0448-11de-a6fe-93d51630548a --- .../gatk/walkers/indels/IndelRealigner.java | 4 +-- .../indels/IndelRealignerIntegrationTest.java | 33 ++++++++++--------- 2 files changed, 19 insertions(+), 18 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java index 598a1f9eb..c0b170d25 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java @@ -98,8 +98,8 @@ public class IndelRealigner extends ReadWalker { protected ConstrainedMateFixingManager manager = null; protected SAMFileWriter writerToUse = null; - @Argument(fullName = "consensusDeterminationModel", shortName = "model", doc = "How should we determine the possible alternate consenses? -- in the order of least permissive to most permissive there is KNOWNS_ONLY (use only indels from known indels provided in RODs), USE_READS (additionally use indels already present in the original alignments of the reads), and USE_SW (additionally use 'Smith-Waterman' to generate alternate consenses). The default is USE_SW", required = false) - public ConsensusDeterminationModel consensusModel = ConsensusDeterminationModel.USE_SW; + @Argument(fullName = "consensusDeterminationModel", shortName = "model", doc = "How should we determine the possible alternate consenses? -- in the order of least permissive to most permissive there is KNOWNS_ONLY (use only indels from known indels provided in RODs), USE_READS (additionally use indels already present in the original alignments of the reads), and USE_SW (additionally use 'Smith-Waterman' to generate alternate consenses). The default is USE_READS", required = false) + public ConsensusDeterminationModel consensusModel = ConsensusDeterminationModel.USE_READS; // ADVANCED OPTIONS FOLLOW diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java index 3e8ec3e02..0c841d746 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java @@ -15,7 +15,8 @@ public class IndelRealignerIntegrationTest extends WalkerTest { private static final String knownIndels = validationDataLocation + "indelRealignerTest.pilot1.ceu.vcf"; private static final String baseCommandPrefix = "-T IndelRealigner -noPG -R " + b36KGReference + " -I " + mainTestBam + " -targetIntervals " + mainTestIntervals + " -compress 0 -L 20:49,500-55,500 "; private static final String baseCommand = baseCommandPrefix + "-o %s "; - private static final String base_md5 = "d7c7acd346ee4c8d34f1e2499ff7c313"; + private static final String base_md5 = "e041186bca9dccf360747c89be8417ad"; + private static final String base_md5_with_SW_or_VCF = "d7c7acd346ee4c8d34f1e2499ff7c313"; @Test public void testDefaults() { @@ -29,7 +30,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest { WalkerTestSpec spec2 = new WalkerTestSpec( baseCommand + "-B:indels,vcf " + knownIndels, 1, - Arrays.asList(base_md5)); + Arrays.asList(base_md5_with_SW_or_VCF)); executeTest("test realigner defaults with VCF", spec2); WalkerTestSpec spec3 = new WalkerTestSpec( @@ -56,25 +57,25 @@ public class IndelRealignerIntegrationTest extends WalkerTest { } @Test - public void testReadsOnly() { + public void testUseSW() { WalkerTestSpec spec1 = new WalkerTestSpec( - baseCommand + "--consensusDeterminationModel USE_READS -B:indels,vcf " + knownIndels, + baseCommand + "--consensusDeterminationModel USE_SW -B:indels,vcf " + knownIndels, 1, - Arrays.asList(base_md5)); - executeTest("realigner known indels only from VCF", spec1); + Arrays.asList(base_md5_with_SW_or_VCF)); + executeTest("realigner use SW from VCF", spec1); WalkerTestSpec spec2 = new WalkerTestSpec( - baseCommand + "--consensusDeterminationModel USE_READS -D " + GATKDataLocation + "dbsnp_129_b36.rod", + baseCommand + "--consensusDeterminationModel USE_SW -D " + GATKDataLocation + "dbsnp_129_b36.rod", 1, - Arrays.asList("e041186bca9dccf360747c89be8417ad")); - executeTest("realigner known indels only from dbsnp", spec2); + Arrays.asList(base_md5_with_SW_or_VCF)); + executeTest("realigner use SW from dbsnp", spec2); } @Test public void testLods() { HashMap e = new HashMap(); e.put( "-LOD 60", base_md5 ); - e.put( "-LOD 1", "f158f18198cf48bbb3d4f1b7127928a3" ); + e.put( "-LOD 1 --consensusDeterminationModel USE_SW", "f158f18198cf48bbb3d4f1b7127928a3" ); for ( Map.Entry entry : e.entrySet() ) { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( @@ -90,14 +91,14 @@ public class IndelRealignerIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( "-T IndelRealigner -noPG -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10,000,000-11,000,000 -targetIntervals " + validationDataLocation + "indelRealignerTest.NA12878.chrom1.intervals -compress 0 -o %s", 1, - Arrays.asList("be859f9a98d738becee0526887cae42e")); + Arrays.asList("fe39c007d287d372a8137d11c60fbc50")); executeTest("realigner long run", spec); } @Test public void testNoTags() { WalkerTestSpec spec = new WalkerTestSpec( - baseCommand + "--noOriginalAlignmentTags", + baseCommand + "--noOriginalAlignmentTags --consensusDeterminationModel USE_SW", 1, Arrays.asList("e77e59cc6363cf58f392ce5ea8d7e0b6")); executeTest("realigner no output tags", spec); @@ -108,21 +109,21 @@ public class IndelRealignerIntegrationTest extends WalkerTest { WalkerTestSpec spec1 = new WalkerTestSpec( baseCommandPrefix + "-stats %s -o /dev/null", 1, - Arrays.asList("ed5a207ddf5bdda4bb76899fb3eae35c")); + Arrays.asList("7ed8d4eed635613fd031598a5c9ef5a3")); executeTest("realigner stats", spec1); WalkerTestSpec spec2 = new WalkerTestSpec( baseCommandPrefix + "-LOD 60 -stats %s -o /dev/null", 1, - Arrays.asList("ffab7d9ca19daa8a21e0b8f0072d39e9")); + Arrays.asList("e8b02bfc5debec55fe936a38c59463cc")); executeTest("realigner stats", spec2); } @Test public void testMaxReadsInMemory() { HashMap e = new HashMap(); - e.put( "--maxReadsInMemory 10000", "d7c7acd346ee4c8d34f1e2499ff7c313" ); - e.put( "--maxReadsInMemory 40000", base_md5 ); + e.put( "--maxReadsInMemory 10000", base_md5 ); + e.put( "--maxReadsInMemory 40000", base_md5 ); for ( Map.Entry entry : e.entrySet() ) { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(