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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
This commit is contained in:
kiran 2010-08-08 07:03:37 +00:00
parent e242a8f143
commit 758ab428f5
1 changed files with 5 additions and 5 deletions
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10
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
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@ -96,18 +96,18 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
// Finally, warn the user about any leftover sample expressions that had no effect // Finally, warn the user about any leftover sample expressions that had no effect
if (sampleExpressionsThatDidNotWork.size() > 0) { if (sampleExpressionsThatDidNotWork.size() > 0) {
logger.warn("The following arguments to --sample did not work:");
for (String exp : sampleExpressionsThatDidNotWork) { 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 { } else {
samples.addAll(vcfSamples); samples.addAll(vcfSamples);
} }
for (String sample : samples) {
logger.info("Including sample '" + sample + "'");
}
Set<VCFHeaderLine> headerLines = VCFUtils.smartMergeHeaders(vcfRods.values(), logger); Set<VCFHeaderLine> headerLines = VCFUtils.smartMergeHeaders(vcfRods.values(), logger);
headerLines.add(new VCFHeaderLine("source", "SelectVariants")); headerLines.add(new VCFHeaderLine("source", "SelectVariants"));
vcfWriter.writeHeader(new VCFHeader(headerLines, samples)); vcfWriter.writeHeader(new VCFHeader(headerLines, samples));