From 6ed71cf683696c539c75eadcbf4f9d45a4c63997 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 24 May 2011 20:12:27 +0000
Subject: [PATCH] Annotation that adds a list of samples who are polymorphic at
 a site based on the GTs.  Very useful if you are looking at rare variants
 among many samples, esp. in Evoker

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5868 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/annotator/SampleList.java    | 71 +++++++++++++++++++
 1 file changed, 71 insertions(+)
 create mode 100755 java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java
new file mode 100755
index 000000000..3c1c87170
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java
@@ -0,0 +1,71 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.gatk.walkers.annotator;
+
+import org.broad.tribble.util.variantcontext.Genotype;
+import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broad.tribble.vcf.VCFHeaderLineType;
+import org.broad.tribble.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
+import org.broadinstitute.sting.utils.MathUtils;
+import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
+
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+
+public class SampleList implements InfoFieldAnnotation {
+
+    public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
+        if ( vc.isMonomorphic() || !vc.hasGenotypes() )
+            return null;
+
+        StringBuffer samples = new StringBuffer();
+        for ( Genotype genotype : vc.getGenotypesSortedByName() ) {
+            if ( genotype.isCalled() && !genotype.isHomRef() ){
+                if ( samples.length() > 0 )
+                    samples.append(",");
+                samples.append(genotype.getSampleName());
+            }
+        }
+
+        if ( samples.length() == 0 )
+            return null;
+
+        Map<String, Object> map = new HashMap<String, Object>();
+        map.put("Samples", samples.toString());
+        return map;
+    }
+
+    public List<String> getKeyNames() { return Arrays.asList("Samples"); }
+
+    public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("Samples", VCFInfoHeaderLine.UNBOUNDED, VCFHeaderLineType.String, "List of polymorphic samples")); }
+}