From 0d209d5442d6c7370ea891ef832219e6426f9fc3 Mon Sep 17 00:00:00 2001 From: depristo Date: Sat, 14 Aug 2010 16:02:13 +0000 Subject: [PATCH] Nicer printing out of clustering git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4035 348d0f76-0448-11de-a6fe-93d51630548a --- .../variantrecalibration/ApplyVariantCuts.java | 16 ++++++++++++---- 1 file changed, 12 insertions(+), 4 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyVariantCuts.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyVariantCuts.java index b3f03b8a0..684f6d115 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyVariantCuts.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyVariantCuts.java @@ -126,17 +126,25 @@ public class ApplyVariantCuts extends RodWalker { public void initialize() { - // todo -- ryan, it's always best to use a read data structure, I need to read these in. + // todo -- ryan, it's always best to use a data structure, I need to read these in too. // todo -- I would have updated your code but there's no integration test to protect me from unexpected effects boolean firstLine = true; try { for( final String line : new XReadLines(new File( TRANCHE_FILENAME )) ) { if( !firstLine ) { final String[] vals = line.split(","); - if(Double.parseDouble(vals[0]) >= FDR_FILTER_LEVEL) { - qCuts.add(Double.parseDouble(vals[2])); - filterName.add(vals[4]); + double FDR = Double.parseDouble(vals[0]); + double TsTv = Double.parseDouble(vals[1]); + double pCut = Double.parseDouble(vals[2]); + String name = vals[4]; + //String statusMsg = "Excluding, below FDR level"; + if (FDR >= FDR_FILTER_LEVEL) { + qCuts.add(pCut); + filterName.add(name); + //statusMsg = "Keeping, above FDR threshold"; } + logger.info(String.format("Tranche %s with %.2f FDR, TsTv %.2f and pCut %.2f, threshold %.2f", + name, FDR, TsTv, pCut, FDR_FILTER_LEVEL)); } firstLine = false; }