From 1011f3862ba7ac3d7b4cebb4f28e1603c84be6f1 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Thu, 8 Mar 2012 08:57:29 -0500 Subject: [PATCH] CalibrateGenotypeLikelihoods now emits the position of the variant for debugging -- Refactored some duplicated code (FYI, code duplication = root of all evil) into shared functions -- Added long-missing integrationtests -- CHRIS/RYAN -- it would be very good to add an integration test covering external VCF files as I believe we rely on this functionality and it's not tested at all --- public/java/test/org/broadinstitute/sting/BaseTest.java | 2 ++ 1 file changed, 2 insertions(+) diff --git a/public/java/test/org/broadinstitute/sting/BaseTest.java b/public/java/test/org/broadinstitute/sting/BaseTest.java index bc4ce098b..e33f6717a 100755 --- a/public/java/test/org/broadinstitute/sting/BaseTest.java +++ b/public/java/test/org/broadinstitute/sting/BaseTest.java @@ -61,6 +61,8 @@ public abstract class BaseTest { public static final String annotationDataLocation = GATKDataLocation + "Annotations/"; public static final String b37GoodBAM = validationDataLocation + "/CEUTrio.HiSeq.b37.chr20.10_11mb.bam"; + public static final String b37GoodNA12878BAM = validationDataLocation + "/NA12878.HiSeq.WGS.bwa.cleaned.recal.hg19.20.bam"; + public static final String b37_NA12878_OMNI = validationDataLocation + "/NA12878.omni.vcf"; public static final String refseqAnnotationLocation = annotationDataLocation + "refseq/"; public static final String hg18Refseq = refseqAnnotationLocation + "refGene-big-table-hg18.txt";