From f47f640df6328b2a020f61892795ee48daab1afd Mon Sep 17 00:00:00 2001 From: depristo Date: Thu, 16 Apr 2009 21:54:56 +0000 Subject: [PATCH] Better debugging output and testing git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@455 348d0f76-0448-11de-a6fe-93d51630548a --- java/src/org/broadinstitute/sting/utils/GenomeLoc.java | 8 ++++++-- python/ValidateGATK.py | 2 +- testdata/ValidatingPileupTargets.list | 4 ++-- 3 files changed, 9 insertions(+), 5 deletions(-) diff --git a/java/src/org/broadinstitute/sting/utils/GenomeLoc.java b/java/src/org/broadinstitute/sting/utils/GenomeLoc.java index 21afae47e..e2d92d48e 100644 --- a/java/src/org/broadinstitute/sting/utils/GenomeLoc.java +++ b/java/src/org/broadinstitute/sting/utils/GenomeLoc.java @@ -61,7 +61,10 @@ public class GenomeLoc implements Comparable { public static int getContigIndex( final String contig ) { assert contigInfo.getSequenceIndex(contig) != -1 : "Unknown contig " + contig; - + + if (contigInfo.getSequenceIndex(contig) == -1) + Utils.scareUser(String.format("Contig %s given as location, but this contig isn't present in the Fasta sequence dictionary", contig)); + return contigInfo.getSequenceIndex(contig); } @@ -342,8 +345,9 @@ public class GenomeLoc implements Comparable { // public final String getContig() { assert this.contigIndex != -1; - + assert contigInfo.getSequence(this.contigIndex) != null; assert contigInfo.getSequence(this.contigIndex).getSequenceName() != null; + return contigInfo.getSequence(this.contigIndex).getSequenceName(); //if (contigInfo != null && contigInfo.getSequence(this.contigIndex) != null) { // return contigInfo.getSequence(this.contigIndex).getSequenceName(); diff --git a/python/ValidateGATK.py b/python/ValidateGATK.py index 9c883fea6..22fe9fefe 100755 --- a/python/ValidateGATK.py +++ b/python/ValidateGATK.py @@ -95,7 +95,7 @@ def main(): if not os.path.exists(validationOutput) or OPTIONS.ignoreExistingFiles: analysis = "ValidatingPileup" - cmd = "java -jar ~/dev/GenomeAnalysisTK/trunk/dist/GenomeAnalysisTK.jar -T " + analysis + " -I " + subBAM + " -R " + ref + " -l INFO -S SILENT -U -B pileup SAMPileup " + pileup + cmd = "java -ea -Xmx1024m -jar ~/dev/GenomeAnalysisTK/trunk/dist/GenomeAnalysisTK.jar -T " + analysis + " -I " + subBAM + " -R " + ref + " -l INFO -S SILENT -U -B pileup SAMPileup " + pileup print cmd farm_commands.cmd(cmd, OPTIONS.farmQueue, outputFile=validationOutput) diff --git a/testdata/ValidatingPileupTargets.list b/testdata/ValidatingPileupTargets.list index 68f524ca1..4acba65ac 100755 --- a/testdata/ValidatingPileupTargets.list +++ b/testdata/ValidatingPileupTargets.list @@ -5,10 +5,10 @@ /broad/1KG/DCC/data/NA12878/alignment/NA12878.chrom6.SRP000032.2009_02.bam /broad/1KG/reference/human_b36_both.fasta 6:1-10,000,00 # daughter chrom 1 deep coverage -/broad/1KG/DCC/data/NA12878/alignment/NA12878.chrom1.SRP000032.2009_02.bam /broad/1KG/reference/human_b36_female.fasta * +/broad/1KG/DCC/data/NA12878/alignment/NA12878.chrom1.SRP000032.2009_02.bam /broad/1KG/reference/human_b36_both.fasta * # mother of trio individual low coverage -/broad/1KG/DCC/data/NA12892/alignment/NA12892.SRP000031.2009_02.bam /broad/1KG/reference/human_b36_female.fasta * +/broad/1KG/DCC/data/NA12892/alignment/NA12892.SRP000031.2009_02.bam /broad/1KG/reference/human_b36_both.fasta * # Pilot 3 /broad/1KG/pilot3/sams/NA12892.bam /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta *