From dec0a781c2de1902638ad0e47bf91b4645f1ee66 Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 2 Dec 2009 20:19:28 +0000
Subject: [PATCH] Un-reinventing the wheel.  --sleep argument removed.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2227 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/GATKArgumentCollection.java     |  7 -------
 .../sting/gatk/GenomeAnalysisEngine.java       |  8 --------
 .../gatk/walkers/annotator/SecondBaseSkew.java | 18 ------------------
 3 files changed, 33 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/GATKArgumentCollection.java b/java/src/org/broadinstitute/sting/gatk/GATKArgumentCollection.java
index 9de3779e7..945a0a69a 100755
--- a/java/src/org/broadinstitute/sting/gatk/GATKArgumentCollection.java
+++ b/java/src/org/broadinstitute/sting/gatk/GATKArgumentCollection.java
@@ -64,10 +64,6 @@ public class GATKArgumentCollection {
     @Argument(fullName = "intervals", shortName = "L", doc = "A list of genomic intervals over which to operate. Can be explicitly specified on the command line or in a file.", required = false)
     public List<String> intervals = null;
 
-    @ElementList(required = false)
-    @Argument(fullName = "sleep", doc = "If provided, the engine will sleep for this number of milliseconds before starting the analysis -- useful for debugging", required = false)
-    public long sleep = 0;
-
     @Element(required = false)
     @Argument(fullName = "reference_sequence", shortName = "R", doc = "Reference sequence file", required = false)
     public File referenceFile = null;
@@ -223,9 +219,6 @@ public class GATKArgumentCollection {
         if (other.walkerArgs.size() != walkerArgs.size()) {
             return false;
         }
-        if (other.sleep != sleep) {
-            return false;
-        }
         for (String s : walkerArgs.keySet()) {
             if (!other.walkerArgs.containsKey(s)) {
                 return false;
diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
index 5f6af06f1..910d0914f 100755
--- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
@@ -136,14 +136,6 @@ public class GenomeAnalysisEngine {
         // save our argument parameter
         this.argCollection = args;
 
-        if ( args.sleep > 0 ) {
-            try {
-                Thread.sleep(args.sleep);
-            } catch ( InterruptedException e ) {
-                throw new RuntimeException(e);
-            }
-        }
-
         // Prepare the data for traversal.
         initializeDataSources(my_walker, filters, argCollection);
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkew.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkew.java
index 93b854733..35fd2aa23 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkew.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkew.java
@@ -33,13 +33,6 @@ public class SecondBaseSkew implements VariantAnnotation {
     public String annotate(ReferenceContext ref, ReadBackedPileup pileup, Variation variation, List<Genotype> genotypes) {
         if ( variation.isSNP() && variation.isBiallelic() ) {
             char snp = variation.getAlternativeBaseForSNP();
-//            try {
-//                System.out.printf("snp %c, alt is %c%n", snp, getNonref(genotypes, ref.getBase()));
-//            } catch (IllegalStateException e) {
-//                System.out.printf("%s is not biallelic%n", variation.toString());
-//                return null;
-//            }
-
             Pair<Integer,Double> depthProp = getSecondaryPileupNonrefEstimator(ref.getBase(), pileup, snp);
             if ( depthProp == null ) {
                 return null;
@@ -79,21 +72,10 @@ public class SecondBaseSkew implements VariantAnnotation {
         }
 
         if ( variantDepth > 0 ) {
-            //System.out.printf("%d %d %d %d%n", primaryPileup.length, secondaryPileup.length, variantDepth, variantsWithRefSecondBase );
             double biasedProportion = ( 1.0 + variantsWithRefSecondBase )/(1.0 + variantDepth );
             return new Pair<Integer,Double>(variantDepth+1, biasedProportion);
         } else {
             return null;
         }
     }
-
-    private char getNonref(List<Genotype> genotypes, char ref) {
-        for ( Genotype g : genotypes ) {
-            if ( g.isVariant(ref) ) {
-                return g.toVariation(ref).getAlternativeBaseForSNP();
-            }
-        }
-
-        throw new IllegalStateException("List of genotypes did not contain a variant.");
-    }
 }