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VariantFiltration moved to core. 

Another win for the team.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1517 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-09-03 15:41:41 +00:00
parent 5130ca9b94
commit 5bd99fc1c4
20 changed files with 20 additions and 20 deletions
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2
java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/IVFBinomialStrand.java → java/src/org/broadinstitute/sting/gatk/walkers/filters/IVFBinomialStrand.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.variants; package org.broadinstitute.sting.gatk.walkers.filters;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.contexts.VariantContext; import org.broadinstitute.sting.gatk.contexts.VariantContext;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/IVFNull.java → java/src/org/broadinstitute/sting/gatk/walkers/filters/IVFNull.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.variants; package org.broadinstitute.sting.gatk.walkers.filters;
public class IVFNull implements IndependentVariantFeature { public class IVFNull implements IndependentVariantFeature {
public void initialize(String arguments) {} public void initialize(String arguments) {}

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/IVFPrimaryBases.java → java/src/org/broadinstitute/sting/gatk/walkers/filters/IVFPrimaryBases.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.variants; package org.broadinstitute.sting.gatk.walkers.filters;
import org.broadinstitute.sting.gatk.contexts.VariantContext; import org.broadinstitute.sting.gatk.contexts.VariantContext;
import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.MathUtils;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/IVFSecondaryBases.java → java/src/org/broadinstitute/sting/gatk/walkers/filters/IVFSecondaryBases.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.variants; package org.broadinstitute.sting.gatk.walkers.filters;
import org.broadinstitute.sting.gatk.contexts.VariantContext; import org.broadinstitute.sting.gatk.contexts.VariantContext;
import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.MathUtils;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/IndependentVariantFeature.java → java/src/org/broadinstitute/sting/gatk/walkers/filters/IndependentVariantFeature.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.variants; package org.broadinstitute.sting.gatk.walkers.filters;
/** /**
* Interface for conditionally independent variant features. * Interface for conditionally independent variant features.

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/RatioFilter.java → java/src/org/broadinstitute/sting/gatk/walkers/filters/RatioFilter.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.variants; package org.broadinstitute.sting.gatk.walkers.filters;
import org.broadinstitute.sting.gatk.contexts.VariantContext; import org.broadinstitute.sting.gatk.contexts.VariantContext;
import org.broadinstitute.sting.gatk.refdata.rodVariants; import org.broadinstitute.sting.gatk.refdata.rodVariants;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECAlleleBalance.java → java/src/org/broadinstitute/sting/gatk/walkers/filters/VECAlleleBalance.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.variants; package org.broadinstitute.sting.gatk.walkers.filters;
import org.broadinstitute.sting.gatk.refdata.rodVariants; import org.broadinstitute.sting.gatk.refdata.rodVariants;
import org.broadinstitute.sting.utils.ReadBackedPileup; import org.broadinstitute.sting.utils.ReadBackedPileup;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECClusteredSnps.java → java/src/org/broadinstitute/sting/gatk/walkers/filters/VECClusteredSnps.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.variants; package org.broadinstitute.sting.gatk.walkers.filters;
import org.broadinstitute.sting.gatk.contexts.VariantContext; import org.broadinstitute.sting.gatk.contexts.VariantContext;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECDepthOfCoverage.java → java/src/org/broadinstitute/sting/gatk/walkers/filters/VECDepthOfCoverage.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.variants; package org.broadinstitute.sting.gatk.walkers.filters;
import org.broadinstitute.sting.gatk.contexts.VariantContext; import org.broadinstitute.sting.gatk.contexts.VariantContext;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECFisherStrand.java → java/src/org/broadinstitute/sting/gatk/walkers/filters/VECFisherStrand.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.variants; package org.broadinstitute.sting.gatk.walkers.filters;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.VariantContext; import org.broadinstitute.sting.gatk.contexts.VariantContext;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECHomopolymer.java → java/src/org/broadinstitute/sting/gatk/walkers/filters/VECHomopolymer.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.variants; package org.broadinstitute.sting.gatk.walkers.filters;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.VariantContext; import org.broadinstitute.sting.gatk.contexts.VariantContext;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECIndelArtifact.java → java/src/org/broadinstitute/sting/gatk/walkers/filters/VECIndelArtifact.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.variants; package org.broadinstitute.sting.gatk.walkers.filters;
import org.broadinstitute.sting.gatk.contexts.VariantContext; import org.broadinstitute.sting.gatk.contexts.VariantContext;
import org.broadinstitute.sting.gatk.refdata.*; import org.broadinstitute.sting.gatk.refdata.*;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECLodThreshold.java → java/src/org/broadinstitute/sting/gatk/walkers/filters/VECLodThreshold.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.variants; package org.broadinstitute.sting.gatk.walkers.filters;
import org.broadinstitute.sting.gatk.contexts.VariantContext; import org.broadinstitute.sting.gatk.contexts.VariantContext;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECMappingQuality.java → java/src/org/broadinstitute/sting/gatk/walkers/filters/VECMappingQuality.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.variants; package org.broadinstitute.sting.gatk.walkers.filters;
import org.broadinstitute.sting.gatk.contexts.VariantContext; import org.broadinstitute.sting.gatk.contexts.VariantContext;
import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.MathUtils;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECMappingQualityZero.java → java/src/org/broadinstitute/sting/gatk/walkers/filters/VECMappingQualityZero.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.variants; package org.broadinstitute.sting.gatk.walkers.filters;
import org.broadinstitute.sting.gatk.contexts.VariantContext; import org.broadinstitute.sting.gatk.contexts.VariantContext;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECNull.java → java/src/org/broadinstitute/sting/gatk/walkers/filters/VECNull.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.variants; package org.broadinstitute.sting.gatk.walkers.filters;
public class VECNull implements VariantExclusionCriterion { public class VECNull implements VariantExclusionCriterion {
public void initialize(String arguments) { public void initialize(String arguments) {

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECOnOffGenotypeRatio.java → java/src/org/broadinstitute/sting/gatk/walkers/filters/VECOnOffGenotypeRatio.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.variants; package org.broadinstitute.sting.gatk.walkers.filters;
import org.broadinstitute.sting.gatk.refdata.rodVariants; import org.broadinstitute.sting.gatk.refdata.rodVariants;
import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.*;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VariantContextWindow.java → java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantContextWindow.java
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@ -23,7 +23,7 @@
* OTHER DEALINGS IN THE SOFTWARE. * OTHER DEALINGS IN THE SOFTWARE.
*/ */
package org.broadinstitute.sting.playground.gatk.walkers.variants; package org.broadinstitute.sting.gatk.walkers.filters;
import org.broadinstitute.sting.gatk.contexts.VariantContext; import org.broadinstitute.sting.gatk.contexts.VariantContext;
import org.broadinstitute.sting.utils.StingException; import org.broadinstitute.sting.utils.StingException;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VariantExclusionCriterion.java → java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantExclusionCriterion.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.variants; package org.broadinstitute.sting.gatk.walkers.filters;
public interface VariantExclusionCriterion { public interface VariantExclusionCriterion {
public void initialize(String arguments); public void initialize(String arguments);

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VariantFiltrationWalker.java → java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.variants; package org.broadinstitute.sting.gatk.walkers.filters;
import org.broadinstitute.sting.gatk.contexts.*; import org.broadinstitute.sting.gatk.contexts.*;
import org.broadinstitute.sting.gatk.refdata.*; import org.broadinstitute.sting.gatk.refdata.*;