From 956c36a2c810209caab63b0abb81708a02516472 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 11 Dec 2009 17:32:47 +0000
Subject: [PATCH] Help for the qc package.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2327 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/qc/PrintLocusContextWalker.java   | 7 ++-----
 .../sting/gatk/walkers/qc/ReadValidationWalker.java      | 9 +++------
 .../sting/gatk/walkers/qc/ValidatingPileupWalker.java    | 8 +++-----
 3 files changed, 8 insertions(+), 16 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintLocusContextWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintLocusContextWalker.java
index cd0165b1a..fb01a51d2 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintLocusContextWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintLocusContextWalker.java
@@ -11,11 +11,8 @@ import java.util.Arrays;
 import net.sf.samtools.SAMRecord;
 
 /**
- * Created by IntelliJ IDEA.
- * User: hanna
- * Date: 13 Apr, 2009
- * Time: 11:23:14 AM
- * To change this template use File | Settings | File Templates.
+ * Diagnostics analysis.  At each locus in the input data set, prints the reference base, genomic location, and
+ * all aligning reads in a compact but human-readable form. 
  */
 public class PrintLocusContextWalker extends LocusWalker<AlignmentContext, Integer> implements TreeReducible<Integer> {
     public AlignmentContext map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java
index f44dbc75f..59dc30070 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java
@@ -37,12 +37,9 @@ import java.util.ArrayList;
  */
 
 /**
- * 
- * @author aaron 
- * 
- * Class ReadValidationWalker
- *
- * A descriptions should go here. Blame aaron if it's missing.
+ * Diagnostics analysis.  Checks all reads passed through the system to ensure that
+ * the same read is not passed to the walker multiple consecutive times.
+ * @author aaron
  */
 public class ReadValidationWalker extends ReadWalker<SAMRecord, SAMRecord> {
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java
index e86a1f358..eb077dbb4 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java
@@ -14,11 +14,9 @@ import org.broadinstitute.sting.utils.StingException;
 import java.util.Arrays;
 
 /**
- * Created by IntelliJ IDEA.
- * User: mdepristo
- * Date: Feb 22, 2009
- * Time: 3:22:14 PM
- * To change this template use File | Settings | File Templates.
+ * Diagnostics analysis.  At every locus in the input set, compares the pileup data (reference base, aligned base from
+ * each overlapping read, and quality score) to the reference pileup data generated by samtools.  Samtools' pileup data
+ * should be specified using the command-line argument '-B pileup,SAMPileup,<your sam pileup file>'.
  */
 @Requires(value={DataSource.READS,DataSource.REFERENCE},referenceMetaData=@RMD(name="pileup",type=rodSAMPileup.class))
 public class ValidatingPileupWalker extends LocusWalker<Integer, ValidationStats>  implements TreeReducible<ValidationStats> {