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Minor cleanup

This commit is contained in:
Eric Banks 2011-08-09 23:28:59 -04:00
parent bc2d4f554d
commit 1ea5ec276b
2 changed files with 0 additions and 17 deletions
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16
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
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@ -36,7 +36,6 @@ import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.io.StingSAMFileWriter; import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.gatk.walkers.BAQMode; import org.broadinstitute.sting.gatk.walkers.BAQMode;
import org.broadinstitute.sting.gatk.walkers.ReadWalker; import org.broadinstitute.sting.gatk.walkers.ReadWalker;
@ -159,21 +158,6 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
protected boolean CHECKEARLY = false; protected boolean CHECKEARLY = false;
// DEPRECATED
@Deprecated
@Argument(fullName="sortInCoordinateOrderEvenThoughItIsHighlyUnsafe", doc="This argument is no longer used.", required=false)
protected boolean DEPRECATED_SORT_IN_COORDINATE_ORDER = false;
@Deprecated
@Argument(fullName="realignReadsWithBadMates", doc="This argument is no longer used.", required=false)
protected boolean DEPRECATED_REALIGN_MATES = false;
@Deprecated
@Argument(fullName="useOnlyKnownIndels", shortName="knownsOnly", doc="This argument is no longer used. See --consensusDeterminationModel instead.", required=false)
protected boolean DEPRECATED_KNOWNS_ONLY = false;
// DEBUGGING OPTIONS FOLLOW // DEBUGGING OPTIONS FOLLOW
@Hidden @Hidden

1
public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
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@ -1,7 +1,6 @@
package org.broadinstitute.sting.gatk.walkers.indels; package org.broadinstitute.sting.gatk.walkers.indels;
import org.broadinstitute.sting.WalkerTest; import org.broadinstitute.sting.WalkerTest;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.testng.annotations.Test; import org.testng.annotations.Test;
import java.util.Arrays; import java.util.Arrays;