Documentation and cleanup.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1946 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/alignment/bwa/AlignmentValidationWalker.java

@@ -14,12 +14,20 @@ import net.sf.samtools.SAMRecord;
  * @version 0.1
  */
 public class AlignmentValidationWalker 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 instance used to generate alignments.
+     */
     private BWACAligner aligner = null;
 
-
+    /**
+     * Create an aligner object.  The aligner object will load and hold the BWT until close() is called.
+     */
     @Override
     public void initialize() {
         aligner = new BWACAligner(prefix + ".ann",
@@ -31,8 +39,12 @@ public class AlignmentValidationWalker extends ReadWalker<Integer,Integer> {
                                   prefix + ".rsa");        
     }
 
-    public Integer reduceInit() { return 0; }
-
+    /**
+     * 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 reads aligned by this map (aka 1).
+     */
     @Override
     public Integer map(char[] ref, SAMRecord read) {
         byte[] bases = read.getReadBases();
@@ -45,7 +57,8 @@ public class AlignmentValidationWalker extends ReadWalker<Integer,Integer> {
             matches = false;
         else {
             for(Alignment alignment: alignments) {
-                matches = (alignment.getAlignmentStart() == read.getAlignmentStart());
+                matches = (alignment.getContigIndex() == read.getReferenceIndex());
+                matches &= (alignment.getAlignmentStart() == read.getAlignmentStart());
                 matches &= (alignment.isNegativeStrand() == read.getReadNegativeStrandFlag());
                 matches &= (alignment.getCigar().equals(read.getCigar()));
                 matches &= (alignment.getMappingQuality() == read.getMappingQuality());
@@ -59,10 +72,28 @@ public class AlignmentValidationWalker extends ReadWalker<Integer,Integer> {
         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();

java/src/org/broadinstitute/sting/alignment/bwa/AlignmentWalker.java

@@ -1,16 +1,13 @@
 package org.broadinstitute.sting.alignment.bwa;
 
 import org.broadinstitute.sting.utils.cmdLine.Argument;
-import org.broadinstitute.sting.utils.BaseUtils;
-import org.broadinstitute.sting.utils.StingException;
-import org.broadinstitute.sting.alignment.Alignment;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import net.sf.samtools.SAMRecord;
 
 import java.util.Random;
 
 /**
- * Javadoc goes here.
+ * Align reads to the reference specified by BWTPrefix.
  *
  * @author mhanna
  * @version 0.1
@@ -29,6 +26,9 @@ public class AlignmentWalker extends ReadWalker<Integer,Integer> {
      */
     private Random random = new Random();
 
+    /**
+     * Create an aligner object.  The aligner object will load and hold the BWT until close() is called.
+     */    
     @Override
     public void initialize() {
         aligner = new BWACAligner(prefix + ".ann",
@@ -40,20 +40,42 @@ public class AlignmentWalker extends ReadWalker<Integer,Integer> {
                                   prefix + ".rsa");
     }
 
-    public Integer reduceInit() { return 0; }
-
+    /**
+     * 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) {
         SAMRecord[] alignedReads = aligner.align(read);
         SAMRecord selectedRead = alignedReads[random.nextInt(alignedReads.length)];
         out.println(selectedRead.format());
-        return 1;
+        return alignedReads.length;
     }
 
+    /**
+     * Initial value for reduce.  In this case, alignments will be counted.
+     * @return 0, indicating no alignments yet found.
+     */
+    @Override
+    public Integer reduceInit() { return 0; }
+
+    /**
+     * Calculates the number of alignments found.
+     * @param value Number of alignments found by this map.
+     * @param sum Number of alignments found before this map.
+     * @return Number of alignments found 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();