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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
This commit is contained in:
Mark DePristo 2012-03-08 08:57:29 -05:00
parent 8158348e01
commit 1011f3862b
1 changed files with 2 additions and 0 deletions
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public/java/test/org/broadinstitute/sting/BaseTest.java
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@ -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";