From 178ba24c27af683602b34cc6e6b3d685b896db54 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Fri, 30 Sep 2011 10:28:18 -0400 Subject: [PATCH] Move getSamplesForSamFile to SampleUtils -- A nearly identical piece of code already lived in SampleUtils. Now there are two functions, one taking a regular header and another grabbing the merged header from the GATK engine itself. Much cleaner --- .../sting/gatk/GenomeAnalysisEngine.java | 7 ------- .../org/broadinstitute/sting/utils/SampleUtils.java | 12 ++++++++++++ 2 files changed, 12 insertions(+), 7 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java index 050128740..4884452d2 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java @@ -1041,13 +1041,6 @@ public class GenomeAnalysisEngine { return this.sampleDataSource; } - /** - * Returns all samples that were referenced in the SAM file - */ - public Set getSAMFileSamples() { - return sampleDataSource.getSamples(SampleUtils.getSAMFileSamples(getSAMFileHeader())); - } - public Map getApproximateCommandLineArguments(Object... argumentProviders) { return CommandLineUtils.getApproximateCommandLineArguments(parsingEngine,argumentProviders); } diff --git a/public/java/src/org/broadinstitute/sting/utils/SampleUtils.java b/public/java/src/org/broadinstitute/sting/utils/SampleUtils.java index 1b4703e4a..edc1413ba 100755 --- a/public/java/src/org/broadinstitute/sting/utils/SampleUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/SampleUtils.java @@ -69,6 +69,18 @@ public class SampleUtils { return samples; } + + /** + * Same as @link getSAMFileSamples but gets all of the samples + * in the SAM files loaded by the engine + * + * @param engine + * @return + */ + public final static Set getSAMFileSamples(GenomeAnalysisEngine engine) { + return SampleUtils.getSAMFileSamples(engine.getSAMFileHeader()); + } + /** * Gets all of the unique sample names from all VCF rods input by the user *