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Better debugging output and testing 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@455 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-04-16 21:54:56 +00:00
parent 165e504d1c
commit f47f640df6
3 changed files with 9 additions and 5 deletions
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8
java/src/org/broadinstitute/sting/utils/GenomeLoc.java
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@ -61,7 +61,10 @@ public class GenomeLoc implements Comparable<GenomeLoc> {
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<GenomeLoc> {
//
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();

2
python/ValidateGATK.py
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@ -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)

4
testdata/ValidatingPileupTargets.list vendored
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@ -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 *