From 2901299ff6dc680e2164ce16b7bb1490aeb3878d Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 27 Jan 2011 01:38:26 +0000
Subject: [PATCH] Sets the number of samples to all of the samples in the file
 when it's not specifed on the command-line explicitly.  GenotypeConcordance
 no longer a standard evaluation.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5094 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../newvarianteval/NewVariantEvalWalker.java      | 15 ++++++++++-----
 .../evaluators/GenotypeConcordance.java           |  2 +-
 2 files changed, 11 insertions(+), 6 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/NewVariantEvalWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/NewVariantEvalWalker.java
index 60f4e371a..e8a84e075 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/NewVariantEvalWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/NewVariantEvalWalker.java
@@ -90,6 +90,7 @@ public class NewVariantEvalWalker extends RodWalker<Integer, Integer> implements
     private Set<String> knownNames = new TreeSet<String>();
     private Set<String> evalNames = new TreeSet<String>();
     private Set<String> sampleNames = new TreeSet<String>();
+    private int numSamples = 0;
 
     // The list of stratifiers and evaluators to use
     private TreeSet<VariantStratifier> stratificationObjects = null;
@@ -366,13 +367,17 @@ public class NewVariantEvalWalker extends RodWalker<Integer, Integer> implements
         // Now that we have all the rods categorized, determine the sample list from the eval rods.
         Map<String, VCFHeader> vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit(), evalNames);
         Set<String> vcfSamples = SampleUtils.getSampleList(vcfRods, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE);
-        sampleNames.add(ALL_SAMPLE_NAME);
 
         // If we're not using the per-sample stratification, don't bother loading the sample list
         if (Arrays.asList(STRATIFICATIONS_TO_USE).contains("Sample")) {
             sampleNames.addAll(SampleUtils.getSamplesFromCommandLineInput(vcfSamples, SAMPLE_EXPRESSIONS));
+            numSamples = sampleNames.size();
+        } else {
+            numSamples = vcfSamples.size();
         }
 
+        sampleNames.add(ALL_SAMPLE_NAME);
+
         // Initialize select expressions
         jexlExpressions.addAll(VariantContextUtils.initializeMatchExps(SELECT_NAMES, SELECT_EXPS));
 
@@ -491,10 +496,10 @@ public class NewVariantEvalWalker extends RodWalker<Integer, Integer> implements
                 }
 
                 if ( trackName.contains("eval") ) {
-                    vc = getSubsetOfVariantContext(vc, sampleNamesMinusAll);
+                    VariantContext vcsub = (sampleNamesMinusAll.size() > 0) ? getSubsetOfVariantContext(vc, sampleNamesMinusAll) : vc;
 
-                    if (byFilter || !vc.isFiltered()) {
-                        vcs.put(ALL_SAMPLE_NAME, vc);
+                    if (byFilter || !vcsub.isFiltered()) {
+                        vcs.put(ALL_SAMPLE_NAME, vcsub);
                     }
                 }
 
@@ -601,7 +606,7 @@ public class NewVariantEvalWalker extends RodWalker<Integer, Integer> implements
      * @return the number of samples
      */
     public int getNumSamples() {
-        return sampleNames.size();
+        return numSamples;
     }
 
     /**
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/GenotypeConcordance.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/GenotypeConcordance.java
index 416ec34d9..354b61d9c 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/GenotypeConcordance.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/evaluators/GenotypeConcordance.java
@@ -44,7 +44,7 @@ import java.util.*;
  */
 
 @Analysis(name = "Genotype Concordance", description = "Determine the genotype concordance between the genotypes in difference tracks")
-public class GenotypeConcordance extends VariantEvaluator implements StandardEval {
+public class GenotypeConcordance extends VariantEvaluator {
     private static final boolean PRINT_INTERESTING_SITES = true;
 
     protected final static Logger logger = Logger.getLogger(GenotypeConcordance.class);