From c93a611ea3b987f611bd7e7b2a41984f13c93dba Mon Sep 17 00:00:00 2001 From: Geraldine Van der Auwera Date: Wed, 20 Jan 2016 15:28:41 -0500 Subject: [PATCH] Remove unneeded dependency Addresses https://github.com/broadgsa/gatk/pull/15 for Guillermo --- .../gatk/tools/walkers/varianteval/VariantEval.java | 3 +-- .../org/broadinstitute/gatk/utils/SequenceDictionaryUtils.java | 2 +- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEval.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEval.java index 1617f4f39..120c4caf9 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEval.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEval.java @@ -29,7 +29,6 @@ import com.google.java.contract.Requires; import htsjdk.samtools.reference.IndexedFastaSequenceFile; import htsjdk.samtools.util.IntervalTree; import htsjdk.samtools.SAMSequenceRecord; -import oracle.jrockit.jfr.StringConstantPool; import org.apache.log4j.Logger; import htsjdk.tribble.Feature; import org.broadinstitute.gatk.engine.samples.Trio; @@ -755,4 +754,4 @@ public class VariantEval extends RodWalker implements TreeRedu public boolean ignoreAC0Sites() { return ! keepSitesWithAC0; } -} \ No newline at end of file +} diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtils.java index 4d46e17fe..8eaa8c42b 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtils.java @@ -177,7 +177,7 @@ public class SequenceDictionaryUtils { case OUT_OF_ORDER: { UserException ex = new UserException.IncompatibleSequenceDictionaries( - "The contig order in " + name1 + " and " + name2 + "is not " + "The contig order in " + name1 + " and " + name2 + " is not " + "the same; to fix this please see: " + "(https://www.broadinstitute.org/gatk/guide/article?id=1328), " + " which describes reordering contigs in BAM and VCF files.",