From bdd0a6f9fa0ca37b9d8c858a271ea195bee576a0 Mon Sep 17 00:00:00 2001 From: depristo Date: Thu, 3 Sep 2009 13:43:10 +0000 Subject: [PATCH] change to make build work git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1511 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/datasources/providers/LocusView.java | 2 +- testdata/ValidatingPileupTargets.list | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java b/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java index 5ce839a41..76170832e 100755 --- a/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java @@ -61,7 +61,7 @@ public abstract class LocusView extends LocusIterator implements View { Iterator reads = new FilteringIterator(provider.getReadIterator(), new LocusStreamFilterFunc()); this.sourceInfo = provider.getReadIterator().getSourceInfo(); - if (GenomeAnalysisEngine.instance.getArguments().useLocusIteratorByState) + if ( GenomeAnalysisEngine.instance != null && GenomeAnalysisEngine.instance.getArguments().useLocusIteratorByState) this.loci = new LocusIteratorByState(reads, sourceInfo); else this.loci = new LocusIteratorByHanger(reads, sourceInfo); diff --git a/testdata/ValidatingPileupTargets.list b/testdata/ValidatingPileupTargets.list index 612aacaf1..fd07dc132 100755 --- a/testdata/ValidatingPileupTargets.list +++ b/testdata/ValidatingPileupTargets.list @@ -2,13 +2,13 @@ /humgen/gsa-scr1/GATK_Data/Validation_Data/MV1994.bam /humgen/gsa-scr1/GATK_Data/Validation_Data/Escherichia_coli_K12_MG1655.fasta * # daughter chrom 6 deep coverage first 10 MB -/broad/1KG/DCC/data/NA12878/alignment/NA12878.chrom6.SLX.SRP000032.2009_06.bam /broad/1KG/reference/human_b36_both.fasta 6:1-10,000,00 +/broad/1KG/DCC/ftp/pilot_data/NA12878/alignment/NA12878.chrom6.SLX.SRP000032.2009_06.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.SLX.SRP000032.2009_06.bam /broad/1KG/reference/human_b36_both.fasta * +/broad/1KG/DCC/ftp/pilot_data/NA12878/alignment/NA12878.chrom1.SLX.SRP000032.2009_06.bam /broad/1KG/reference/human_b36_both.fasta * # mother of trio individual low coverage -/broad/1KG/DCC/data/NA12892/alignment/NA12892.SLX.SRP000031.2009_06.bam /broad/1KG/reference/human_b36_both.fasta * +/broad/1KG/DCC/ftp/pilot_data/NA12892/alignment/NA12892.SLX.SRP000031.2009_06.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 *