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OPAL-2875 - call to bcftools view command to filter sample ids #4

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merged 1 commit into from
Mar 21, 2017
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OPAL-2875 - call to bcftools view command to filter sample ids #4

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14 changes: 14 additions & 0 deletions jennite-vcf-store/src/main/java/org/obiba/jennite/vcf/JenniteVCFStore.java
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Original file line number Diff line number Diff line change
Expand Up @@ -232,6 +232,20 @@ public void readVCFStatistics(String vcfName, OutputStream out) throws NoSuchEle
Files.copy(getStatsFile(vcfName).toPath(), out);
}

@Override
public void filter(String vcfName, Format format, String commaSeparatedSampleIds, File destination) throws NoSuchElementException, IOException {
if (!hasVCF(vcfName)) throw new NoSuchElementException("No VCF with name '" + vcfName + "' can be found");
String outputType = Format.VCF == format ? "-Oz" : "-Ob";
int status = runProcess(vcfName, bcftools("view",
"--force-samples",
outputType,
"-s",
commaSeparatedSampleIds,
getVCFGZFile(vcfName).getAbsolutePath(),
"-o", destination.getAbsolutePath()));
if (status != 0) throw new VCFStoreException("VCF/BCF file sample id filter using bcftools failed");
}

//
// Private methods
//
Expand Down