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My own integration test isn't passing with a clean checkout. This fix to the walker ought to do it.

This commit is contained in:
Christopher Hartl 2012-09-12 10:11:06 -04:00
parent 546586b70e
commit 96be1cbea9
1 changed files with 9 additions and 7 deletions
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16
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
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@ -396,10 +396,17 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
commandLineUniqueSamples.addAll(samplesFromExpressions); commandLineUniqueSamples.addAll(samplesFromExpressions);
commandLineUniqueSamples.addAll(sampleNames); commandLineUniqueSamples.addAll(sampleNames);
commandLineUniqueSamples.removeAll(vcfSamples); commandLineUniqueSamples.removeAll(vcfSamples);
// second, add the requested samples
samples.addAll(sampleNames);
samples.addAll(samplesFromExpressions);
samples.addAll(samplesFromFile);
logger.debug(Utils.join(",",commandLineUniqueSamples));
if ( commandLineUniqueSamples.size() > 0 && ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES ) { if ( commandLineUniqueSamples.size() > 0 && ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES ) {
logger.warn("Samples present on command line input that are not present in the VCF. These samples will be ignored."); logger.warn("Samples present on command line input that are not present in the VCF. These samples will be ignored.");
samplesFromFile.removeAll(commandLineUniqueSamples); samples.removeAll(commandLineUniqueSamples);
samplesFromExpressions.retainAll(commandLineUniqueSamples);
} else if (commandLineUniqueSamples.size() > 0 ) { } else if (commandLineUniqueSamples.size() > 0 ) {
throw new UserException.BadInput(String.format("%s%n%n%s%n%n%s%n%n%s", throw new UserException.BadInput(String.format("%s%n%n%s%n%n%s%n%n%s",
"Samples entered on command line (through -sf or -sn) that are not present in the VCF.", "Samples entered on command line (through -sf or -sn) that are not present in the VCF.",
@ -408,11 +415,6 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
"To ignore these samples, run with --ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES")); "To ignore these samples, run with --ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES"));
} }
// second, add the requested samples
samples.addAll(sampleNames);
samples.addAll(samplesFromExpressions);
samples.addAll(samplesFromFile);
samples.removeAll(commandLineUniqueSamples);
// if none were requested, we want all of them // if none were requested, we want all of them
if ( samples.isEmpty() ) { if ( samples.isEmpty() ) {