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Adding a TODO for future consideration 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5821 348d0f76-0448-11de-a6fe-93d51630548a
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ebanks 2011-05-19 15:02:23 +00:00
parent 0bb6b9a91a
commit bc98ac1e74
1 changed files with 2 additions and 0 deletions
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java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
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@ -150,6 +150,8 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
Map<String, VCFHeader> vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit(), rodNames); Map<String, VCFHeader> vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit(), rodNames);
Set<String> vcfSamples = SampleUtils.getSampleList(vcfRods, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE); Set<String> vcfSamples = SampleUtils.getSampleList(vcfRods, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE);
// TODO -- This causes the sample ordering in the VCF to be "random" (i.e. whatever order they are pulled from the HashSet).
// TODO -- We should either enforce alphabetical ordering here (as with other walkers) or base it on the order from the command-line - but we shouldn't leave this up to Java to decide.
samples = SampleUtils.getSamplesFromCommandLineInput(vcfSamples, SAMPLE_EXPRESSIONS); samples = SampleUtils.getSamplesFromCommandLineInput(vcfSamples, SAMPLE_EXPRESSIONS);
for (String sample : samples) { for (String sample : samples) {
logger.info("Including sample '" + sample + "'"); logger.info("Including sample '" + sample + "'");