From 4bfec4c55b750674e01715ce36298a1087e972f6 Mon Sep 17 00:00:00 2001 From: hanna Date: Mon, 23 May 2011 21:32:53 +0000 Subject: [PATCH] Reenabling E.coli ValidatingPileup with MV1994 realigned using the BWA/C bindings. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5856 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/refdata/features/sampileup/SAMPileupCodec.java | 2 +- .../gatk/walkers/qc/ValidatingPileupIntegrationTest.java | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/features/sampileup/SAMPileupCodec.java b/java/src/org/broadinstitute/sting/gatk/refdata/features/sampileup/SAMPileupCodec.java index 9a2f36e5b..00b7c45d9 100644 --- a/java/src/org/broadinstitute/sting/gatk/refdata/features/sampileup/SAMPileupCodec.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/features/sampileup/SAMPileupCodec.java @@ -108,7 +108,7 @@ public class SAMPileupCodec implements FeatureCodec { if ( feature.getRef() == '*' ) { parseIndels(observedString,feature) ; if ( feature.isDeletion() ) feature.setEnd(feature.getStart()+feature.length()-1); - else feature.setEnd(feature.getStart()-1); // if it's not a deletion and we are biallelic, this got to be an insertion; otherwise the state is inconsistent!!!! + else feature.setEnd(feature.getStart()); // if it's not a deletion and we are biallelic, this got to be an insertion; otherwise the state is inconsistent!!!! } else { parseBasesAndQuals(feature,tokens[8],tokens[9]); // if the variant is a SNP or a reference base (i.e. no variant at all) diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupIntegrationTest.java index 7c47d437c..c5cdf9f02 100644 --- a/java/test/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupIntegrationTest.java @@ -12,14 +12,14 @@ import java.util.Collections; * @version 0.1 */ public class ValidatingPileupIntegrationTest extends WalkerTest { - @Test(enabled = false) + @Test(enabled = true) public void testEcoliThreaded() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T ValidatingPileup" + " -I " + validationDataLocation + "MV1994.selected.bam" + " -R " + validationDataLocation + "Escherichia_coli_K12_MG1655.fasta" + " -B:pileup,SAMPileup "+ validationDataLocation + "MV1994.selected.pileup" + - " -S SILENT -nt 8 -U ALLOW_SEQ_DICT_INCOMPATIBILITY",0, Collections.emptyList()); + " -S SILENT -nt 8",0, Collections.emptyList()); executeTest("testEcoliThreaded",spec); } }