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change to make build work 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1511 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-09-03 13:43:10 +00:00
parent b01ac9de0c
commit bdd0a6f9fa
2 changed files with 4 additions and 4 deletions
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2
java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java
View File

@ -61,7 +61,7 @@ public abstract class LocusView extends LocusIterator implements View {
Iterator<SAMRecord> 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);

6
testdata/ValidatingPileupTargets.list vendored
View File

@ -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 *