From ee2abd30c477e662e33860d0fdcef1effdec3398 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 23 Nov 2009 16:37:59 +0000
Subject: [PATCH] Count the best alignments and emit them to a file.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2118 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../alignment/CountBestAlignmentsWalker.java  | 90 +++++++++++++++++++
 1 file changed, 90 insertions(+)
 create mode 100644 java/src/org/broadinstitute/sting/alignment/CountBestAlignmentsWalker.java

diff --git a/java/src/org/broadinstitute/sting/alignment/CountBestAlignmentsWalker.java b/java/src/org/broadinstitute/sting/alignment/CountBestAlignmentsWalker.java
new file mode 100644
index 000000000..3fdd46952
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/alignment/CountBestAlignmentsWalker.java
@@ -0,0 +1,90 @@
+package org.broadinstitute.sting.alignment;
+
+import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.alignment.bwa.BWTFiles;
+import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
+import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
+import org.broadinstitute.sting.utils.cmdLine.Argument;
+import net.sf.samtools.SAMRecord;
+
+import java.util.*;
+
+/**
+ * Counts the number of best alignments
+ *
+ * @author mhanna
+ * @version 0.1
+ */
+public class CountBestAlignmentsWalker extends ReadWalker<Integer,Integer> {
+    /**
+     * The supporting BWT index generated using BWT.
+     */
+    @Argument(fullName="BWTPrefix",shortName="BWT",doc="Index files generated by bwa index -d bwtsw",required=false)
+    String prefix = "/Users/mhanna/reference/Ecoli/Escherichia_coli_K12_MG1655.fasta";
+
+    /**
+     * The actual aligner.
+     */
+    private Aligner aligner = null;
+
+    private SortedMap<Integer,Integer> alignmentFrequencies = new TreeMap<Integer,Integer>();
+
+    /**
+     * Create an aligner object.  The aligner object will load and hold the BWT until close() is called.
+     */
+    @Override
+    public void initialize() {
+        BWTFiles bwtFiles = new BWTFiles(prefix);
+        BWAConfiguration configuration = new BWAConfiguration();
+        aligner = new BWACAligner(bwtFiles,configuration);
+    }
+
+    /**
+     * Aligns a read to the given reference.
+     * @param ref Reference over the read.  Read will most likely be unmapped, so ref will be null.
+     * @param read Read to align.
+     * @return Number of alignments found for this read.
+     */
+    @Override
+    public Integer map(char[] ref, SAMRecord read) {
+        Iterator<Alignment[]> alignmentIterator = aligner.getAllAlignments(read.getReadBases()).iterator();
+        if(alignmentIterator.hasNext()) {
+            int numAlignments = alignmentIterator.next().length;
+            if(alignmentFrequencies.containsKey(numAlignments))
+                alignmentFrequencies.put(numAlignments,alignmentFrequencies.get(numAlignments)+1);
+            else
+                alignmentFrequencies.put(numAlignments,1);
+        }
+        return 1;
+    }    
+
+    /**
+     * Initial value for reduce.  In this case, validated reads will be counted.
+     * @return 0, indicating no reads yet validated.
+     */
+    @Override
+    public Integer reduceInit() { return 0; }
+
+    /**
+     * Calculates the number of reads processed.
+     * @param value Number of reads processed by this map.
+     * @param sum Number of reads processed before this map.
+     * @return Number of reads processed up to and including this map.
+     */
+    @Override
+    public Integer reduce(Integer value, Integer sum) {
+        return value + sum;
+    }
+
+    /**
+     * Cleanup.
+     * @param result Number of reads processed.
+     */
+    @Override
+    public void onTraversalDone(Integer result) {
+        aligner.close();
+        for(Map.Entry<Integer,Integer> alignmentFrequency: alignmentFrequencies.entrySet())
+            out.printf("%d\t%d%n", alignmentFrequency.getKey(), alignmentFrequency.getValue());
+        super.onTraversalDone(result);
+    }
+}