From 610cc7ae2bca0ecbec782a3cba4cc754f2be13e4 Mon Sep 17 00:00:00 2001 From: chartl Date: Tue, 29 Jun 2010 22:42:04 +0000 Subject: [PATCH] Cool package trick Kiran showed me. VariantEvaluator no longer public, AAT specifies the core package even though it lives in oneoffs. Disabled so integration tests pass. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3677 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/varianteval/VariantEvaluator.java | 2 +- .../walkers/varianteval/AminoAcidTransition.java | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvaluator.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvaluator.java index e5f7abf0f..961459745 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvaluator.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvaluator.java @@ -14,7 +14,7 @@ import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext; * This software is supplied without any warranty or guaranteed support whatsoever. Neither * the Broad Institute nor MIT can be responsible for its use, misuse, or functionality. */ -public abstract class VariantEvaluator { +abstract class VariantEvaluator { // protected boolean accumulateInterestingSites = false, printInterestingSites = false; // protected String interestingSitePrefix = null; protected boolean processedASite = false; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/AminoAcidTransition.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/AminoAcidTransition.java index 45406f758..cab8c1dc0 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/AminoAcidTransition.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/AminoAcidTransition.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.oneoffprojects.walkers.varianteval; +package org.broadinstitute.sting.gatk.walkers.varianteval; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; @@ -150,7 +150,7 @@ public class AminoAcidTransition extends VariantEvaluator { } public boolean enabled() { - return true; + return false; } public String toString() { @@ -189,4 +189,4 @@ public class AminoAcidTransition extends VariantEvaluator { //public void finalizeEvaluation() { // //} -} \ No newline at end of file +}