From b88dec387c6850c41430b87ee8a8279986f3f9d1 Mon Sep 17 00:00:00 2001 From: rpoplin Date: Tue, 3 May 2011 20:35:30 +0000 Subject: [PATCH] clean up from VQSR movement git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5741 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java | 2 +- .../sting/gatk/walkers/varianteval/VariantEvalWalker.java | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java index 45575827c..98ec7f3d7 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java @@ -41,7 +41,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.gatk.walkers.RMD; import org.broadinstitute.sting.gatk.walkers.Requires; -import org.broadinstitute.sting.playground.gatk.walkers.variantrecalibration.VQSRCalibrationCurve; +import org.broadinstitute.sting.gatk.walkers.variantrecalibration.VQSRCalibrationCurve; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.SampleUtils; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java index c4b61b2eb..4c15a4406 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java @@ -174,10 +174,10 @@ public class VariantEvalWalker extends RodWalker implements Tr // Add select expressions for anything in the tranches file if ( TRANCHE_FILENAME != null ) { // we are going to build a few select names automatically from the tranches file - for ( Tranche t : Tranche.readTraches(new File(TRANCHE_FILENAME)) ) { + for ( Tranche t : Tranche.readTranches(new File(TRANCHE_FILENAME)) ) { logger.info("Adding select for all variant above the pCut of : " + t); SELECT_EXPS.add(String.format(VariantRecalibrator.VQS_LOD_KEY + " >= %.2f", t.minVQSLod)); - SELECT_NAMES.add(String.format("FDR-%.2f", t.fdr)); + SELECT_NAMES.add(String.format("TS-%.2f", t.ts)); } }