From 7140280bf640fe2e46de52c51888134210dddf6e Mon Sep 17 00:00:00 2001 From: Guillermo del Angel Date: Wed, 20 Jul 2011 10:44:37 -0400 Subject: [PATCH] Further bug fixes/cleanups for PrintReadsWalker --- .../sting/gatk/walkers/PrintReadsWalker.java | 14 +++----------- 1 file changed, 3 insertions(+), 11 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java index 2b7db8d34..7e1dcd707 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java @@ -114,17 +114,9 @@ public class PrintReadsWalker extends ReadWalker { } if (SAMPLES_SPECIFIED ) { // user specified samples to select - String readSample = read.getReadGroup().getSample(); - boolean found = false; - for (String sampleSelected : samplesToChoose) { - if (readSample.equalsIgnoreCase(sampleSelected)) { - found = true; - break; - } - - } - - if (!found) + // todo - should be case-agnostic but for simplicity and speed this is ignored. + // todo - can check at initialization intersection of requested samples and samples in BAM header to further speedup. + if (!samplesToChoose.contains(read.getReadGroup().getSample())) return false; }