From 23d96b1d432c05c47722c9a010aba11c3fcf7261 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 11 Dec 2009 16:01:25 +0000
Subject: [PATCH] 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
---
 .../sting/alignment/AlignmentValidationWalker.java            | 4 +++-
 .../org/broadinstitute/sting/alignment/AlignmentWalker.java   | 3 ++-
 .../sting/alignment/CountBestAlignmentsWalker.java            | 3 ++-
 java/src/org/broadinstitute/sting/alignment/package-info.java | 4 ++++
 4 files changed, 11 insertions(+), 3 deletions(-)
 create mode 100644 java/src/org/broadinstitute/sting/alignment/package-info.java

diff --git a/java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java b/java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java
index 116803ed6..646d055d6 100644
--- a/java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java
+++ b/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
diff --git a/java/src/org/broadinstitute/sting/alignment/AlignmentWalker.java b/java/src/org/broadinstitute/sting/alignment/AlignmentWalker.java
index 8fb2f5061..ee22a2e20 100644
--- a/java/src/org/broadinstitute/sting/alignment/AlignmentWalker.java
+++ b/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
diff --git a/java/src/org/broadinstitute/sting/alignment/CountBestAlignmentsWalker.java b/java/src/org/broadinstitute/sting/alignment/CountBestAlignmentsWalker.java
index 30d892d71..fd87e710e 100644
--- a/java/src/org/broadinstitute/sting/alignment/CountBestAlignmentsWalker.java
+++ b/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
diff --git a/java/src/org/broadinstitute/sting/alignment/package-info.java b/java/src/org/broadinstitute/sting/alignment/package-info.java
new file mode 100644
index 000000000..60cf1e425
--- /dev/null
+++ b/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;
\ No newline at end of file