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));