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Remove unneeded dependency 

Addresses https://github.com/broadgsa/gatk/pull/15 for Guillermo
This commit is contained in:
Geraldine Van der Auwera 2016-01-20 15:28:41 -05:00
parent 98eba7fb53
commit c93a611ea3
2 changed files with 2 additions and 3 deletions
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3
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEval.java
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@ -29,7 +29,6 @@ import com.google.java.contract.Requires;
import htsjdk.samtools.reference.IndexedFastaSequenceFile; import htsjdk.samtools.reference.IndexedFastaSequenceFile;
import htsjdk.samtools.util.IntervalTree; import htsjdk.samtools.util.IntervalTree;
import htsjdk.samtools.SAMSequenceRecord; import htsjdk.samtools.SAMSequenceRecord;
import oracle.jrockit.jfr.StringConstantPool;
import org.apache.log4j.Logger; import org.apache.log4j.Logger;
import htsjdk.tribble.Feature; import htsjdk.tribble.Feature;
import org.broadinstitute.gatk.engine.samples.Trio; import org.broadinstitute.gatk.engine.samples.Trio;
@ -755,4 +754,4 @@ public class VariantEval extends RodWalker<Integer, Integer> implements TreeRedu
public boolean ignoreAC0Sites() { public boolean ignoreAC0Sites() {
return ! keepSitesWithAC0; return ! keepSitesWithAC0;
} }
} }

2
public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtils.java
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@ -177,7 +177,7 @@ public class SequenceDictionaryUtils {
case OUT_OF_ORDER: { case OUT_OF_ORDER: {
UserException ex = new UserException.IncompatibleSequenceDictionaries( 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: " + "the same; to fix this please see: "
+ "(https://www.broadinstitute.org/gatk/guide/article?id=1328), " + "(https://www.broadinstitute.org/gatk/guide/article?id=1328), "
+ " which describes reordering contigs in BAM and VCF files.", + " which describes reordering contigs in BAM and VCF files.",