From 75bea4881a3ab9769c773f20a8993402a908e1be Mon Sep 17 00:00:00 2001
From: chartl <chartl@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 16 Jul 2010 21:27:32 +0000
Subject: [PATCH] Modified SampleFilter to allow for multiple samples to be
 given. AminoAcidTransition now turns on when you give VariantEval the right
 commands.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3812 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../broadinstitute/sting/gatk/filters/SampleFilter.java   | 8 +++++---
 .../walkers/varianteval/AminoAcidTransition.java          | 4 +++-
 2 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/filters/SampleFilter.java b/java/src/org/broadinstitute/sting/gatk/filters/SampleFilter.java
index 6fbfa7858..7019fed13 100755
--- a/java/src/org/broadinstitute/sting/gatk/filters/SampleFilter.java
+++ b/java/src/org/broadinstitute/sting/gatk/filters/SampleFilter.java
@@ -30,12 +30,14 @@ import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMReadGroupRecord;
 import org.broadinstitute.sting.commandline.Argument;
 
+import java.util.Set;
+
 public class SampleFilter implements SamRecordFilter {
-    @Argument(fullName = "sample_to_keep", shortName = "goodSM", doc="The name of the sample to keep, filtering out all others", required=true)
-    private String SAMPLE_TO_KEEP = null;
+    @Argument(fullName = "sample_to_keep", shortName = "goodSM", doc="The name of the sample(s) to keep, filtering out all others", required=true)
+    private Set SAMPLES_TO_KEEP = null;
 
     public boolean filterOut( final SAMRecord read ) {
         final SAMReadGroupRecord readGroup = read.getReadGroup();
-        return !( readGroup != null && readGroup.getSample().equals( SAMPLE_TO_KEEP ) );
+        return !( readGroup != null && SAMPLES_TO_KEEP.contains(readGroup.getSample()) );
     }
 }
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/AminoAcidTransition.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/AminoAcidTransition.java
index ea7e0dab9..8954ab45b 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/AminoAcidTransition.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/AminoAcidTransition.java
@@ -127,10 +127,12 @@ public class AminoAcidTransition extends VariantEvaluator {
     private String infoKey;
     private String infoValueSplit;
     private boolean useCodons;
+    private boolean enabled;
     private AminoAcidTable lookup;
 
     public AminoAcidTransition(VariantEvalWalker parent) {
         super(parent);
+        enabled = parent.aminoAcidTransitionKey != null;
         getParsingInformation(parent);
         lookup = new AminoAcidTable();
         acidTable = new AminoAcidTiTvTable();
@@ -160,7 +162,7 @@ public class AminoAcidTransition extends VariantEvaluator {
     }
 
     public boolean enabled() {
-        return false;
+        return enabled;
     }
 
     public String toString() {