From bc98ac1e749ab2d974a9b2bb9424a059019c813d Mon Sep 17 00:00:00 2001 From: ebanks Date: Thu, 19 May 2011 15:02:23 +0000 Subject: [PATCH] Adding a TODO for future consideration git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5821 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/variantutils/SelectVariants.java | 2 ++ 1 file changed, 2 insertions(+) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java index b023f5a8c..a80508715 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java @@ -150,6 +150,8 @@ public class SelectVariants extends RodWalker { Map vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit(), rodNames); Set 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); for (String sample : samples) { logger.info("Including sample '" + sample + "'");