Computes the distribution of insert size per library (for now, one output file per library)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3334 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/MatePairLibrarySize.java

@@ -0,0 +1,83 @@
+package org.broadinstitute.sting.playground.gatk.walkers.diagnostics;
+
+import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.utils.StingException;
+import net.sf.samtools.SAMRecord;
+import net.sf.samtools.SAMReadGroupRecord;
+
+import java.util.*;
+import java.io.File;
+import java.io.PrintWriter;
+import java.io.IOException;
+
+/**
+ * For each sequencing library, outputs the distribution of mate pair sizes
+ */
+public class MatePairLibrarySize extends ReadWalker<Integer, Integer> {
+    @Argument(fullName="outdir", shortName="outdir", doc="Directory to output results")
+    private File OUT_DIR;
+
+    private HashMap<String, HashMap<Integer, Integer>> matePairSize;
+
+    public void initialize() {
+        matePairSize = new HashMap<String, HashMap<Integer, Integer>>();
+
+        for (SAMReadGroupRecord rg : this.getToolkit().getSAMFileHeader().getReadGroups()) {
+            HashMap<Integer, Integer> mps = new HashMap<Integer, Integer>();
+
+            matePairSize.put(rg.getLibrary(), mps);
+        }
+    }
+
+    public boolean filter(char[] ref, SAMRecord read) {
+        return (read.getReadPairedFlag() && read.getFirstOfPairFlag());
+    }
+
+    public Integer map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
+        int insert = read.getInferredInsertSize();
+
+        Integer oldcount = matePairSize.get(read.getReadGroup().getLibrary()).get(insert);
+        if (oldcount == null) { oldcount = 0; }
+
+        matePairSize.get(read.getReadGroup().getLibrary()).put(insert, oldcount + 1);
+
+        return null;
+    }
+
+    public Integer reduceInit() {
+        return null;
+    }
+
+    public Integer reduce(Integer value, Integer sum) {
+        return null;
+    }
+
+    public void onTraversalDone(Integer sum) {
+        String[] libraries = matePairSize.keySet().toArray(new String[1]);
+
+        for (String library : libraries) {
+            try {
+                Integer[] sizes = matePairSize.get(library).keySet().toArray(new Integer[1]);
+
+                if (sizes != null && sizes.length > 1) {
+                    PrintWriter pw = new PrintWriter(String.format("%s/%s.pairdist", OUT_DIR.getAbsolutePath(), library));
+                    Arrays.sort(sizes);
+
+                    pw.printf("%s\t%s%n", "insert", "frequency");
+
+                    for (int insert : sizes) {
+                        if (insert >= 0) {
+                            pw.printf("%d\t%d%n", insert, matePairSize.get(library).get(insert));
+                        }
+                    }
+
+                    pw.close();
+                }
+            } catch (IOException e) {
+                throw new StingException("Unable to initialize output files.");
+            }
+        }
+    }
+}