From 758ab428f5ffed5e3c5c736e85eac7c006760e50 Mon Sep 17 00:00:00 2001 From: kiran Date: Sun, 8 Aug 2010 07:03:37 +0000 Subject: [PATCH] Better logging info for the samples being selected and the sample expressions being ignored. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3978 348d0f76-0448-11de-a6fe-93d51630548a --- .../gatk/walkers/variantutils/SelectVariants.java | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) 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 66c905be9..0bc2019d2 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java @@ -96,18 +96,18 @@ public class SelectVariants extends RodWalker { // Finally, warn the user about any leftover sample expressions that had no effect if (sampleExpressionsThatDidNotWork.size() > 0) { - logger.warn("The following arguments to --sample did not work:"); - for (String exp : sampleExpressionsThatDidNotWork) { - logger.warn("\t" + exp); + logger.warn("The sample expression '" + exp + "' had no effect (no matching sample or pattern match found). Skipping."); } - - logger.warn("Continuing on with the expressions that did work."); } } else { samples.addAll(vcfSamples); } + for (String sample : samples) { + logger.info("Including sample '" + sample + "'"); + } + Set headerLines = VCFUtils.smartMergeHeaders(vcfRods.values(), logger); headerLines.add(new VCFHeaderLine("source", "SelectVariants")); vcfWriter.writeHeader(new VCFHeader(headerLines, samples));