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Fixing the recent SelectVariants fix

This commit is contained in:
Eric Banks 2011-08-20 21:30:08 -04:00
parent 782453235a
commit 0ccd173967
1 changed files with 5 additions and 7 deletions
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12
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
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@ -209,7 +209,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
* Note that sample exclusion takes precedence over inclusion, so that if a sample is in both lists it will be excluded. * Note that sample exclusion takes precedence over inclusion, so that if a sample is in both lists it will be excluded.
*/ */
@Argument(fullName="exclude_sample_file", shortName="xl_sf", doc="File containing a list of samples (one per line) to exclude. Can be specified multiple times", required=false) @Argument(fullName="exclude_sample_file", shortName="xl_sf", doc="File containing a list of samples (one per line) to exclude. Can be specified multiple times", required=false)
public Set<File> XLsampleFiles; public Set<File> XLsampleFiles = new HashSet<File>(0);
/** /**
* Note that these expressions are evaluated *after* the specified samples are extracted and the INFO field annotations are updated. * Note that these expressions are evaluated *after* the specified samples are extracted and the INFO field annotations are updated.
@ -344,12 +344,10 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
} }
// now, exclude any requested samples // now, exclude any requested samples
if (XLsampleFiles != null) Collection<String> XLsamplesFromFile = SampleUtils.getSamplesFromFiles(XLsampleFiles);
if(!XLsampleFiles.isEmpty()) { samples.removeAll(XLsamplesFromFile);
Collection<String> XLsamplesFromFile = SampleUtils.getSamplesFromFiles(XLsampleFiles); samples.removeAll(XLsampleNames);
samples.removeAll(XLsamplesFromFile);
samples.removeAll(XLsampleNames);
}
if ( samples.size() == 0 && !NO_SAMPLES_SPECIFIED ) if ( samples.size() == 0 && !NO_SAMPLES_SPECIFIED )
throw new UserException("All samples requested to be included were also requested to be excluded."); throw new UserException("All samples requested to be included were also requested to be excluded.");