From 0345d9f6a517e08b864dc5eda4b3e57ea2c2e75f Mon Sep 17 00:00:00 2001
From: rpoplin <rpoplin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 26 Jan 2010 14:15:09 +0000
Subject: [PATCH] Updating the recalibrator to use non-depricated getPileup()
 method. Adding documentation to AnalyzeAnnotations so that the walker isn't
 marked as unclean at compile time.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2688 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../recalibration/CovariateCounterWalker.java       |  8 ++++----
 .../variantoptimizer/AnalyzeAnnotationsWalker.java  | 13 +++++++++----
 2 files changed, 13 insertions(+), 8 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java
index cbf75a758..6530a7acb 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java
@@ -47,7 +47,7 @@ import net.sf.samtools.SAMRecord;
 /**
  * This walker is designed to work as the first pass in a two-pass processing step.
  * It does a by-locus traversal operating only at sites that are not in dbSNP.
- * We assume that all reference mismatches we see are therefore errors and indicitive of poor base quality.
+ * We assume that all reference mismatches we see are therefore errors and indicative of poor base quality.
  * This walker generates tables based on various user-specified covariates (such as read group, reported quality score, cycle, and dinucleotide)
  * Since there is a large amount of data one can then calculate an empirical probability of error
  *   given the particular covariates seen at this site, where p(error) = num mismatches / num observations
@@ -238,7 +238,7 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
         }
 
         // Only use data from non-dbsnp sites
-        // Assume every mismatch at a non-dbsnp site is indicitive of poor quality
+        // Assume every mismatch at a non-dbsnp site is indicative of poor quality
         if( !isSNP && ( ++numUnprocessed >= PROCESS_EVERY_NTH_LOCUS ) ) {
             numUnprocessed = 0; // Reset the counter because we are processing this very locus
 
@@ -248,7 +248,7 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
             byte[] bases;
 
             // For each read at this locus
-            for( PileupElement p : context.getPileup() ) {
+            for( PileupElement p : context.getBasePileup() ) {
                 read = p.getRead();
                 offset = p.getOffset();
 
@@ -305,7 +305,7 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
      * @param ref The reference base
      */
     private static void updateMismatchCounts(final Pair<Long, Long> counts, final AlignmentContext context, final char ref) {
-        for( PileupElement p : context.getPileup() ) {
+        for( PileupElement p : context.getBasePileup() ) {
             final char readChar = (char)(p.getBase());
             final int readCharBaseIndex = BaseUtils.simpleBaseToBaseIndex(readChar);
             final int refCharBaseIndex  = BaseUtils.simpleBaseToBaseIndex(ref);
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnalyzeAnnotationsWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnalyzeAnnotationsWalker.java
index f919667a9..58bcf5d38 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnalyzeAnnotationsWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnalyzeAnnotationsWalker.java
@@ -36,9 +36,11 @@ import java.io.IOException;
  */
 
 /**
- * Created by IntelliJ IDEA.
- * User: rpoplin
- * Date: Jan 15, 2010
+ * Takes variant calls as .vcf files and creates plots of truth metrics as a function of the various annotations found in the INFO field.
+ *
+ * @author rpoplin
+ * @since Jan 15, 2010
+ * @help.summary Takes variant calls as .vcf files and creates plots of truth metrics as a function of the various annotations found in the INFO field. 
  */
 
 public class AnalyzeAnnotationsWalker extends RodWalker<Integer, Integer> {
@@ -56,7 +58,7 @@ public class AnalyzeAnnotationsWalker extends RodWalker<Integer, Integer> {
     private int MIN_VARIANTS_PER_BIN = 1000;
     @Argument(fullName = "max_variants_per_bin", shortName = "maxBinSize", doc = "The maximum number of variants in a bin.", required = false)
     private int MAX_VARIANTS_PER_BIN = 20000;
-    @Argument(fullName = "sampleName", shortName = "sampleName", doc = "Only process variants for this sample.", required = false)
+    @Argument(fullName = "sampleName", shortName = "sampleName", doc = "If supplied, only process variants found in this sample.", required = false)
     private String SAMPLE_NAME = null;
 
 
@@ -71,6 +73,9 @@ public class AnalyzeAnnotationsWalker extends RodWalker<Integer, Integer> {
     //
     //---------------------------------------------------------------------------------------------------------------
 
+    /**
+     * Create the output directory and setup the path variables
+     */
     public void initialize() {
 
         // create the output directory where all the data tables and plots will go