Simple IO walker to test / crush file systems and evalute I/O performance in general

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@474 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/playground/gatk/walkers/IOCrusherWalker.java

@@ -0,0 +1,90 @@
+package org.broadinstitute.sting.playground.gatk.walkers;
+
+import org.broadinstitute.sting.gatk.LocusContext;
+import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.utils.cmdLine.Argument;
+import org.broadinstitute.sting.utils.QualityUtils;
+import net.sf.samtools.SAMRecord;
+import net.sf.samtools.SAMFileWriter;
+import net.sf.samtools.SAMFileWriterFactory;
+import net.sf.samtools.SAMFileHeader;
+import edu.mit.broad.picard.reference.ReferenceSequence;
+
+import java.util.ArrayList;
+import java.util.Random;
+import java.io.File;
+
+/**
+ * ReadErrorRateWalker assesses the error rate per read position ('cycle') by comparing the
+ * read to its home on the reference and noting the mismatch rate.  It ignores reads with
+ * indels in them, treats high and low-quality references bases the same, and does not count
+ * ambiguous bases as mismatches.  It's also thread-safe, so you can process a slew of reads
+ * in short order.
+ *
+ * @author Kiran Garimella
+ */
+public class IOCrusherWalker extends ReadWalker<SAMRecord, ArrayList<SAMFileWriter>> {
+    @Argument(shortName="nWaysOut",required=false,defaultValue="1")
+    public int nWaysOut;
+
+    @Argument(shortName="readScaling",required=false,defaultValue="1")
+    public float readScaling;
+
+    @Argument(shortName="outputBase", required=true)
+    public String outputBase;
+
+    public long nReadsRead = 0;
+    public long nReadsWritten = 0;
+
+    /**
+     *
+     */
+    public SAMRecord map(LocusContext context, SAMRecord read) {
+        nReadsRead++;
+        return read;
+    }
+
+    /**
+     * 
+     */
+    public ArrayList<SAMFileWriter> reduceInit() {
+        SAMFileWriterFactory fact = new SAMFileWriterFactory();
+        ArrayList<SAMFileWriter> outputs = new ArrayList<SAMFileWriter>(nWaysOut);
+        for ( int i = 0; i < nWaysOut; i++ ) {
+            SAMFileHeader header = this.getToolkit().getSamReader().getFileHeader();
+            outputs.add(fact.makeBAMWriter(header, true, new File(outputBase + "." + i + ".bam")));
+        }
+        return outputs;
+    }
+
+    /**
+     * Summarize the error rate data.
+     *
+     */
+    public ArrayList<SAMFileWriter> reduce(SAMRecord read, ArrayList<SAMFileWriter> outputs) {
+        for ( SAMFileWriter out : outputs ) {
+            if ( readScaling >= 1.0 ) {
+                int nCopies = (int)Math.ceil(readScaling);
+                for ( int i = 0; i < nCopies; i++) {
+                    out.addAlignment(read);
+                    nReadsWritten++;
+                }
+            } else if ( Math.random() < readScaling ) {
+                out.addAlignment(read);
+                nReadsWritten++;
+            }
+        }
+        
+        return outputs;
+    }
+
+    /**
+     *
+     */
+    public void onTraversalDone(ArrayList<SAMFileWriter> outputs) {
+        for ( SAMFileWriter out : outputs ) {
+            out.close();
+        }
+        System.out.printf("Reads: read %d written %d%n", nReadsRead, nReadsWritten);
+    }
+}