From 5251f49a908b3262ac7ba463bb5451570753d02c Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 19 Oct 2010 03:07:30 +0000
Subject: [PATCH] Including Marian Thieme's BaseCounts class (with some
 modifications)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4522 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/annotator/BaseCounts.java    | 72 +++++++++++++++++++
 1 file changed, 72 insertions(+)
 create mode 100755 java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java
new file mode 100755
index 000000000..5fff0349c
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java
@@ -0,0 +1,72 @@
+/*
+ * Copyright (c) 2010.
+ *
+ * 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.
+ */
+
+// *******************************************************************
+// *                                                                 *
+// * THIS CODE WAS PROVIDED COURTESY OF marian.thieme@googlemail.com *
+// *                                                                 *
+// *******************************************************************
+
+package org.broadinstitute.sting.gatk.walkers.annotator;
+
+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.ReferenceContext;
+import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
+import org.broadinstitute.sting.utils.BaseUtils;
+
+import java.util.Map;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Arrays;
+
+
+public class BaseCounts implements InfoFieldAnnotation {
+
+    public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, VariantContext vc) {
+        if ( stratifiedContexts.size() == 0 )
+            return null;
+
+        int[] counts = new int[4];
+
+        for ( Map.Entry<String, StratifiedAlignmentContext> sample : stratifiedContexts.entrySet() ) {
+            for (byte base : sample.getValue().getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup().getBases() ) {
+                int index = BaseUtils.simpleBaseToBaseIndex(base);
+                if ( index != -1 )
+                    counts[index]++;
+            }
+        }
+        Map<String, Object> map = new HashMap<String, Object>();
+        map.put("BaseCounts", counts);
+        return map;
+    }
+
+    public List<String> getKeyNames() { return Arrays.asList("BaseCounts"); }
+
+    public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("BaseCounts", 4, VCFHeaderLineType.Integer, "Counts of each base")); }
+}
\ No newline at end of file