From c797616c658297563cb95dfd267f5cf9b17b1947 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Thu, 18 Aug 2011 11:51:53 -0400 Subject: [PATCH] If you have one sample in your BAM, getToolkit().getSamples().size() == 2 Also deleted double initializationm, where a line of code was duplicated in creating the GATK engine. --- .../org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java | 2 -- .../sting/gatk/walkers/coverage/CallableLociWalker.java | 4 +++- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java index b0c4e203b..da7eaf6e4 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java @@ -689,8 +689,6 @@ public class GenomeAnalysisEngine { validateSuppliedReads(); readsDataSource = createReadsDataSource(argCollection,genomeLocParser,referenceDataSource.getReference()); - sampleDataSource = new SampleDataSource(getSAMFileHeader(), argCollection.sampleFiles); - for (ReadFilter filter : filters) filter.initialize(this); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalker.java index 3046ef925..98331ec1d 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalker.java @@ -223,8 +223,10 @@ public class CallableLociWalker extends LocusWalker 1 ) + if ( getToolkit().getSamples().size() != 2 ) { + // unbelievably there are actually two samples even when there's just one in the header. God I hate this Samples system throw new UserException.BadArgumentValue("-I", "CallableLoci only works for a single sample, but multiple samples were found in the provided BAM files: " + getToolkit().getSamples()); + } try { PrintStream summaryOut = new PrintStream(summaryFile);