From c78fc23ec5ea34eebaa215f5307dddc2ad18fefe Mon Sep 17 00:00:00 2001 From: rpoplin Date: Thu, 18 Mar 2010 12:46:47 +0000 Subject: [PATCH] Minor updates to output of variant optimizer. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3031 348d0f76-0448-11de-a6fe-93d51630548a --- R/plot_OptimizationCurve.R | 1 + .../variantoptimizer/VariantGaussianMixtureModel.java | 6 +++++- 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/R/plot_OptimizationCurve.R b/R/plot_OptimizationCurve.R index 2618b6abd..c6bc68e67 100755 --- a/R/plot_OptimizationCurve.R +++ b/R/plot_OptimizationCurve.R @@ -10,6 +10,7 @@ targetTITV = as.numeric(args[2]) data = read.table(input,sep=",",head=T) maxVars = max(data$numKnown, data$numNovel) maxTITV = max(data$knownTITV[is.finite(data$knownTITV) & data$numKnown>2000], data$novelTITV[is.finite(data$novelTITV) & data$numNovel > 2000], targetTITV) +maxTITV = min(maxTITV, targetTITV + 1) minTITV = min(data$knownTITV[length(data$knownTITV)], data$novelTITV[length(data$novelTITV)], targetTITV) maxPCut = max(data$pCut[data$numKnown>0 | data$numNovel>0]) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantGaussianMixtureModel.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantGaussianMixtureModel.java index 329cffe87..7bba9b5d2 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantGaussianMixtureModel.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantGaussianMixtureModel.java @@ -328,6 +328,10 @@ public final class VariantGaussianMixtureModel extends VariantOptimizationModel final int numVariants = data.length; final boolean[] markedVariant = new boolean[numVariants]; + for( int iii = 0; iii < numVariants; iii++ ) { + markedVariant[iii] = false; + } + PrintStream outputFile = null; try { outputFile = new PrintStream( outputPrefix + ".dat" ); @@ -368,7 +372,7 @@ public final class VariantGaussianMixtureModel extends VariantOptimizationModel } } if( desiredNumVariants != 0 && !foundDesiredNumVariants && (numKnown + numNovel) >= desiredNumVariants ) { - System.out.println( "Keeping variants with p(true) >= " + String.format("%.1f",pCut) + " results in a filtered set with: " ); + System.out.println( "Keeping variants with QUAL >= " + String.format("%.1f",pCut) + " results in a filtered set with: " ); System.out.println("\t" + numKnown + " known variants"); System.out.println("\t" + numNovel + " novel variants, (dbSNP rate = " + String.format("%.2f",((double) numKnown * 100.0) / ((double) numKnown + numNovel) ) + "%)"); System.out.println("\t" + String.format("%.4f known Ti/Tv ratio", ((double)numKnownTi) / ((double)numKnownTv)));