From b94d8dae17e00412383717f5dd6d6c8378b4c5c0 Mon Sep 17 00:00:00 2001
From: rpoplin <rpoplin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 5 May 2011 20:24:06 +0000
Subject: [PATCH] Removing requirement of providing known track in VQSR for the
 non-humans. Updating placement of legend on tranche plot.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5773 348d0f76-0448-11de-a6fe-93d51630548a
---
 R/plot_Tranches.R                                            | 2 +-
 .../walkers/variantrecalibration/VariantRecalibrator.java    | 5 +----
 2 files changed, 2 insertions(+), 5 deletions(-)

diff --git a/R/plot_Tranches.R b/R/plot_Tranches.R
index 0b0152de3..a79ddd3ab 100755
--- a/R/plot_Tranches.R
+++ b/R/plot_Tranches.R
@@ -66,7 +66,7 @@ barplot(d/1000,horiz=TRUE,col=cols,space=0.2,xlab="Number of Novel Variants (100
 #abline(v= d[2,dim(d)[2]], lty=2)
 #abline(v= d[1,3], lty=2)
 if ( ! suppressLegend ) 
-    legend(5, length(data2$targetTruthSensitivity)-1.25, c('Cumulative TPs','Tranch-specific TPs', 'Tranch-specific FPs', 'Cumulative FPs' ), fill=cols, density=density, bg='white', cex=1.25)
+    legend(3, length(data2$targetTruthSensitivity)/3 +1, c('Cumulative TPs','Tranch-specific TPs', 'Tranch-specific FPs', 'Cumulative FPs' ), fill=cols, density=density, bg='white', cex=1.25)
 
 mtext("Ti/Tv",2,line=2.25,at=length(data2$targetTruthSensitivity)*1.2,las=1, cex=1)
 mtext("truth",2,line=0,at=length(data2$targetTruthSensitivity)*1.2,las=1, cex=1)
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
index b9ff68641..fb6da5ed3 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
@@ -135,9 +135,6 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
         if( !dataManager.checkHasTruthSet() ) {
             throw new UserException.CommandLineException( "No truth set found! Please provide sets of known polymorphic loci marked with the truth=true ROD binding tag. For example, -B:hapmap,VCF,known=false,training=true,truth=true,prior=12.0 hapmapFile.vcf" );
         }
-        if( !dataManager.checkHasKnownSet() ) {
-            throw new UserException.CommandLineException( "No known set found! Please provide sets of known polymorphic loci marked with the known=true ROD binding tag. For example, -B:dbsnp,VCF,known=true,training=false,truth=false,prior=8.0 dbsnpFile.vcf" );
-        }
 
         if( inputNames.size() == 0 ) {
             throw new UserException.BadInput( "No input variant tracks found. Input variant binding names must begin with 'input'." );
@@ -326,7 +323,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
                 for( final VariantDatum datum : randomData ) {
                     stream.print(String.format("%.3f, %.3f, %.3f, %d, %d,", datum.annotations[iii], datum.annotations[jjj], (datum.lod < lodCutoff ? -1.0 : 1.0), datum.usedForTraining, (datum.isKnown ? 1 : -1)));
                 }
-                stream.println("NA,NA,NA,NA,NA)");
+                stream.println("NA,NA,NA,NA,1)");
                 stream.println("d <- matrix(data,ncol=5,byrow=T)");
 
                 final String surfaceFrame = "sf." + USE_ANNOTATIONS[iii] + "." + USE_ANNOTATIONS[jjj];