From 32730b1832fb6a0159289acdccc1e0852a819ab1 Mon Sep 17 00:00:00 2001 From: Guillermo del Angel Date: Wed, 20 Jul 2011 22:17:15 -0400 Subject: [PATCH 1/4] Fixed md5 due to new PL ordering --- .../gatk/walkers/variantutils/BatchMergeIntegrationTest.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/BatchMergeIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/BatchMergeIntegrationTest.java index 7e1d86105..1d4ae0aa8 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/BatchMergeIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/BatchMergeIntegrationTest.java @@ -40,7 +40,7 @@ public class BatchMergeIntegrationTest extends WalkerTest { + " -B:alleles,VCF " + alleles + " -I " + bam, 1, - Arrays.asList("f4ed8f4ef2cba96823c06e90e9d0de35")); + Arrays.asList("8bd114ceaf6a94e96a677fcc52350713")); executeTest("testBatchMerge UG genotype given alleles:" + new File(bam).getName() + " with " + new File(alleles).getName(), spec); } -} \ No newline at end of file +} From 15610ce0c3d3d096d1775afd849f31c489f7e490 Mon Sep 17 00:00:00 2001 From: Christopher Hartl Date: Thu, 21 Jul 2011 11:04:22 -0400 Subject: [PATCH 2/4] Per Matt's request, disabling BWA-based integration tests so he can assess bamboo memory usage. --- .../validation/ValidationAmpliconsIntegrationTest.java | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmpliconsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmpliconsIntegrationTest.java index 6528f5795..1829e9549 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmpliconsIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmpliconsIntegrationTest.java @@ -14,7 +14,7 @@ import java.util.Arrays; */ public class ValidationAmpliconsIntegrationTest extends WalkerTest { - @Test + @Test(enabled=false) public void testWikiExample() { String siteVCF = validationDataLocation + "sites_to_validate.vcf"; String maskVCF = validationDataLocation + "amplicon_mask_sites.vcf"; @@ -27,7 +27,7 @@ public class ValidationAmpliconsIntegrationTest extends WalkerTest { executeTest("Test probes", spec); } - @Test + @Test(enabled=true) public void testWikiExampleNoBWA() { String siteVCF = validationDataLocation + "sites_to_validate.vcf"; String maskVCF = validationDataLocation + "amplicon_mask_sites.vcf"; @@ -40,7 +40,7 @@ public class ValidationAmpliconsIntegrationTest extends WalkerTest { executeTest("Test probes", spec); } - @Test + @Test(enabled=false) public void testWikiExampleMonoFilter() { String siteVCF = validationDataLocation + "sites_to_validate.vcf"; String maskVCF = validationDataLocation + "amplicon_mask_sites.vcf"; From 7054c5342f28f1b5ccb966919dc3a23f06206d0b Mon Sep 17 00:00:00 2001 From: Matt Hanna Date: Thu, 21 Jul 2011 12:13:29 -0400 Subject: [PATCH 3/4] When using the BWA bindings, you have to explicitly call close() to get the bindings to release memory. It may or may not be possible to implicitly close triggered by the GC; I'll add a JIRA. --- .../sting/gatk/walkers/validation/ValidationAmplicons.java | 3 +++ .../validation/ValidationAmpliconsIntegrationTest.java | 4 ++-- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java index 14d462518..7e39d2658 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java @@ -228,6 +228,9 @@ public class ValidationAmplicons extends RodWalker { } public void onTraversalDone(Integer fin ) { + if(aligner != null) + aligner.close(); + validateSequence(); if ( doNotUseBWA ) { lowerRepeats(); diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmpliconsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmpliconsIntegrationTest.java index 1829e9549..95f4ac0ae 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmpliconsIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmpliconsIntegrationTest.java @@ -14,7 +14,7 @@ import java.util.Arrays; */ public class ValidationAmpliconsIntegrationTest extends WalkerTest { - @Test(enabled=false) + @Test(enabled=true) public void testWikiExample() { String siteVCF = validationDataLocation + "sites_to_validate.vcf"; String maskVCF = validationDataLocation + "amplicon_mask_sites.vcf"; @@ -40,7 +40,7 @@ public class ValidationAmpliconsIntegrationTest extends WalkerTest { executeTest("Test probes", spec); } - @Test(enabled=false) + @Test(enabled=true) public void testWikiExampleMonoFilter() { String siteVCF = validationDataLocation + "sites_to_validate.vcf"; String maskVCF = validationDataLocation + "amplicon_mask_sites.vcf"; From 2f5d10d16bd9e53b293c1a913e9f7a3cd601784f Mon Sep 17 00:00:00 2001 From: Christopher Hartl Date: Thu, 21 Jul 2011 13:21:48 -0400 Subject: [PATCH 4/4] Fix bug wherein aligner could be closed prior to its being used to lowercase sequences. --- .../sting/gatk/walkers/validation/ValidationAmplicons.java | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java index 7e39d2658..cb03d4c61 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java @@ -228,14 +228,12 @@ public class ValidationAmplicons extends RodWalker { } public void onTraversalDone(Integer fin ) { - if(aligner != null) - aligner.close(); - validateSequence(); if ( doNotUseBWA ) { lowerRepeats(); } else { lowerNonUniqueSegments(); + aligner.close(); } print(); }