Help system content for the alignment module.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2322 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -12,7 +12,9 @@ import net.sf.samtools.SAMRecord;
 import java.util.Iterator;
 
 /**
- * Validates alignments against existing reads.
+ * Validates consistency of the aligner interface by taking reads already aligned by BWA in a BAM file, stripping them
+ * of their alignment data, realigning them, and making sure one of the best resulting realignments matches the original
+ * alignment from the input file.
  *
  * @author mhanna
  * @version 0.1

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

@@ -12,7 +12,8 @@ import net.sf.picard.reference.ReferenceSequenceFileFactory;
 import java.io.File;
 
 /**
- * Align reads to the reference specified by BWTPrefix.
+ * Aligns reads to a given reference using Heng Li's BWA aligner, presenting the resulting alignments in SAM or BAM format.
+ * Mimics the steps 'bwa aln' followed by 'bwa samse' using the BWA/C implementation.
  *
  * @author mhanna
  * @version 0.1

java/src/org/broadinstitute/sting/alignment/CountBestAlignmentsWalker.java

@@ -10,7 +10,8 @@ import net.sf.samtools.SAMRecord;
 import java.util.*;
 
 /**
- * Counts the number of best alignments
+ * Counts the number of best alignments as presented by BWA and outputs a histogram of number of placements vs. the
+ * frequency of that number of placements.
  *
  * @author mhanna
  * @version 0.1

java/src/org/broadinstitute/sting/alignment/package-info.java

@@ -0,0 +1,4 @@
+/**
+ * Analyses used to validate the correctness and performance the BWA Java bindings.
+ */
+package org.broadinstitute.sting.alignment;