From 7527f950d172f9d25bd4b7af2ba4c25d34896af4 Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 10 May 2010 14:49:38 +0000
Subject: [PATCH] Computes the quality score distribution per readgroup (one
 column per readgroup)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3335 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../diagnostics/QualityScoreDistribution.java | 109 ++++++++++++++++++
 1 file changed, 109 insertions(+)
 create mode 100755 java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/QualityScoreDistribution.java

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/QualityScoreDistribution.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/QualityScoreDistribution.java
new file mode 100755
index 000000000..cce5774fc
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/QualityScoreDistribution.java
@@ -0,0 +1,109 @@
+/*
+ * 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.playground.gatk.walkers.diagnostics;
+
+import org.broadinstitute.sting.gatk.walkers.LocusWalker;
+import org.broadinstitute.sting.gatk.walkers.Reference;
+import org.broadinstitute.sting.gatk.walkers.Window;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.QualityUtils;
+import net.sf.samtools.SAMRecord;
+
+import java.util.*;
+
+/**
+ * Compute quality score distribution
+ */
+public class QualityScoreDistribution extends LocusWalker<Integer, Integer> {
+    private HashMap<String, long[]> qualDists;
+
+    public void initialize() {
+        qualDists = new HashMap<String, long[]>();
+
+        qualDists.put("all", new long[QualityUtils.MAX_QUAL_SCORE]);
+    }
+
+    public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
+        List<SAMRecord> reads = context.getReads();
+        List<Integer> offsets = context.getOffsets();
+
+        for (int i = 0; i < reads.size(); i++) {
+            byte qual = reads.get(i).getBaseQualities()[offsets.get(i)];
+            String name = reads.get(i).getReadGroup().getReadGroupId();
+
+            if (!qualDists.containsKey(name)) {
+                qualDists.put(name, new long[QualityUtils.MAX_QUAL_SCORE]);
+            }
+
+            qualDists.get(name)[qual]++;
+            qualDists.get("all")[qual]++;
+        }
+
+        return null;
+    }
+
+    public Integer reduceInit() {
+        return null;
+    }
+
+    public Integer reduce(Integer value, Integer sum) {
+        return null;
+    }
+
+    public void onTraversalDone(Integer result) {
+        Set<String> names = qualDists.keySet();
+        HashMap<String, Long> norms = new HashMap<String, Long>();
+
+        for (String name : names) {
+            long norm = 0;
+            for (int qual = 0; qual < QualityUtils.MAX_QUAL_SCORE; qual++) {
+                norm += qualDists.get(name)[qual];
+            }
+
+            norms.put(name, norm);
+        }
+
+        out.printf("Q");
+        for (String name : names) {
+            out.printf("\t%s", name);
+        }
+        out.println();
+
+        for (int qual = 0; qual < QualityUtils.MAX_QUAL_SCORE; qual++) {
+            out.printf("%d", qual);
+
+            for (String name : names) {
+                out.printf("\t%f", ((float) qualDists.get(name)[qual])/((float) norms.get(name)));
+            }
+
+            out.println();
+        }
+    }
+}
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