Making ReadLengthDistribution Public

Found this neat little walker Kiran wrote stashed in the private tree. Very useful. Generalized it a bit, added GATKDocs and moved it to public. I might include it as a QC step on the pacbio processing pipeline.
* generalize it so it works with non pair ended reads.
* generalize it to work with no read group information

public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadLengthDistribution.java

@@ -0,0 +1,101 @@
+package org.broadinstitute.sting.gatk.walkers.diagnostics;
+
+import net.sf.samtools.SAMReadGroupRecord;
+import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
+import org.broadinstitute.sting.gatk.report.GATKReport;
+import org.broadinstitute.sting.gatk.report.GATKReportTable;
+import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+
+import java.io.PrintStream;
+import java.util.List;
+
+/**
+ * Outputs the read lengths of all the reads in a file.
+ *
+ *  <p>
+ *     Generates a table with the read lengths categorized per sample. If the file has no sample information
+ *     (no read groups) it considers all reads to come from the same sample.
+ *  </p>
+ *
+ *
+ * <h2>Input</h2>
+ *  <p>
+ *      A BAM file.
+ *  </p>
+ *
+ * <h2>Output</h2>
+ *  <p>
+ *      A human/R readable table of tab separated values with one column per sample and one row per read.
+ *  </p>
+ *
+ * <h2>Examples</h2>
+ *  <pre>
+ *    java
+ *      -jar GenomeAnalysisTK.jar
+ *      -T ReadLengthDistribution
+ *      -I example.bam
+ *      -R reference.fasta
+ *      -o example.tbl
+ *  </pre>
+ *
+ * @author Kiran Garimela
+ */
+
+
+
+public class ReadLengthDistribution extends ReadWalker<Integer, Integer> {
+    @Output
+    public PrintStream out;
+
+    private GATKReport report;
+
+    public void initialize() {
+        report = new GATKReport();
+        report.addTable("ReadLengthDistribution", "Table of read length distributions");
+        GATKReportTable table = report.getTable("ReadLengthDistribution");
+
+        table.addPrimaryKey("readLength");
+
+        List<SAMReadGroupRecord> readGroups = getToolkit().getSAMFileHeader().getReadGroups();
+        if (readGroups.isEmpty())
+            table.addColumn("SINGLE_SAMPLE", 0);
+
+        else
+            for (SAMReadGroupRecord rg : readGroups)
+                table.addColumn(rg.getSample(), 0);
+
+    }
+
+    public boolean filter(ReferenceContext ref, SAMRecord read) {
+        return ( !read.getReadPairedFlag() || read.getReadPairedFlag() && read.getFirstOfPairFlag());
+    }
+
+    @Override
+    public Integer map(ReferenceContext referenceContext, SAMRecord samRecord, ReadMetaDataTracker readMetaDataTracker) {
+        GATKReportTable table = report.getTable("ReadLengthDistribution");
+
+        int length = Math.abs(samRecord.getReadLength());
+        String sample = samRecord.getReadGroup().getSample();
+
+        table.increment(length, sample);
+
+        return null;
+    }
+
+    @Override
+    public Integer reduceInit() {
+        return null;
+    }
+
+    @Override
+    public Integer reduce(Integer integer, Integer integer1) {
+        return null;
+    }
+
+    public void onTraversalDone(Integer sum) {
+        report.print(out);
+    }
+}