From 0ccd1739676b0cf8210df2fc07bff30684390183 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Sat, 20 Aug 2011 21:30:08 -0400 Subject: [PATCH] Fixing the recent SelectVariants fix --- .../gatk/walkers/variantutils/SelectVariants.java | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java index 93bc9e518..bfe7198cf 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java @@ -209,7 +209,7 @@ public class SelectVariants extends RodWalker { * 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) - public Set XLsampleFiles; + public Set XLsampleFiles = new HashSet(0); /** * 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 { } // now, exclude any requested samples - if (XLsampleFiles != null) - if(!XLsampleFiles.isEmpty()) { - Collection XLsamplesFromFile = SampleUtils.getSamplesFromFiles(XLsampleFiles); - samples.removeAll(XLsamplesFromFile); - samples.removeAll(XLsampleNames); - } + Collection XLsamplesFromFile = SampleUtils.getSamplesFromFiles(XLsampleFiles); + samples.removeAll(XLsamplesFromFile); + samples.removeAll(XLsampleNames); + if ( samples.size() == 0 && !NO_SAMPLES_SPECIFIED ) throw new UserException("All samples requested to be included were also requested to be excluded.");