doing some read validation

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1018 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -0,0 +1,144 @@
+package org.broadinstitute.sting.playground.gatk.walkers;
+
+import org.broadinstitute.sting.gatk.walkers.Walker;
+import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.utils.cmdLine.Argument;
+import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.StingException;
+import net.sf.samtools.SAMRecord;
+import net.sf.samtools.SAMFileWriter;
+import net.sf.samtools.SAMReadGroupRecord;
+import net.sf.samtools.SAMFileHeader;
+
+import java.security.MessageDigest;
+import java.security.NoSuchAlgorithmException;
+import java.util.List;
+import java.util.ArrayList;
+import java.math.BigInteger;
+
+
+/*
+ * Copyright (c) 2009 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.
+ */
+
+/**
+ * 
+ * @author aaron 
+ * 
+ * Class ReadValidationWalker
+ *
+ * A descriptions should go here. Blame aaron if it's missing.
+ */
+public class ReadValidationWalker extends ReadWalker<SAMRecord, Integer> {
+
+    // our MD5 sum
+    private MessageDigest m;
+
+    // private list of md5sums
+    private final List<BigInteger> list = new ArrayList<BigInteger>();
+
+    /**
+     * The initialize function.
+     */
+    public void initialize() {
+        try {
+            m = MessageDigest.getInstance("MD5");
+        } catch (NoSuchAlgorithmException e) {
+            throw new StingException("Unable to get the MD5 algorithm. Get a more eXtreme version of JAVA!@!@!!");
+        }
+    }
+
+    /**
+     * The reads filter function.
+     * @param ref the reference bases that correspond to our read, if a reference was provided
+     * @param read the read itself, as a SAMRecord
+     * @return true if the read passes the filter, false if it doesn't
+     */
+    public boolean filter(char[] ref, SAMRecord read) {
+        return true;
+	}
+
+    /**
+     * The reads map function.
+     * @param ref the reference bases that correspond to our read, if a reference was provided
+     * @param read the read itself, as a SAMRecord
+     * @return the read itself
+     */
+    public SAMRecord map( char[] ref, SAMRecord read ) {
+        return read;
+    }
+
+    /**
+     * reduceInit is called once before any calls to the map function.  We use it here to setup the output
+     * bam file, if it was specified on the command line
+     * @return SAMFileWriter, set to the BAM output file if the command line option was set, null otherwise
+     */
+    public Integer reduceInit() {
+        return new Integer(0);
+    }
+
+    /**
+     * given a read and a output location, reduce by emitting the read
+     * @param read the read itself
+     * @param output the output source
+     * @return the SAMFileWriter, so that the next reduce can emit to the same source
+     */
+    public Integer reduce( SAMRecord read, Integer output ) {
+        byte[] ray = new byte[read.getReadName().length() + 5];
+        int x = 0;
+        for (char c: read.getReadName().toCharArray()) {
+            ray[x] = (byte)c;
+            //System.err.println("adding " + c + " to pos " + x);
+            x++;
+        }
+        //System.err.println(read.getReadName() + " name, alignment = " + read.getAlignmentStart());
+        int y = 0;
+        for (;y < 4; y++) {
+            ray[x+y] = (byte)((read.getAlignmentStart() >> y * 8) & 0x000f);    
+        }
+        ray[x+y] = read.getSecondOfPairFlag() ? (byte)1 : (byte)0;
+        BigInteger bigInt = new BigInteger(m.digest(ray));
+        //System.err.println(bigInt.toString());
+        m.reset();
+        if (this.list.contains(bigInt)) {
+            throw new StingException("Seen Read: " + bigInt + "-> " + read.getReadName() + " before (list size = " + list.size() + ")");
+        }
+        if (read.getAlignmentStart() < output) {
+            throw new StingException("Seen Read " + read.getReadName() + " has alignment of " + read.getAlignmentStart() + " before (list size = " + output + ")");
+        }
+        list.add(bigInt);
+        return read.getAlignmentStart();
+    }
+
+
+    /**
+     * when we're done traversing, close the reads file
+     * @param output the SAMFileWriter we've used in the reduce phase
+     */
+    public void onTraversalDone( SAMFileWriter output ) {
+        if (output != null) {
+            output.close();
+        }
+    }
+}