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Moving supported tools to core 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4127 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-08-26 13:56:19 +00:00
parent 45d895dcf4
commit dfae48cee0
16 changed files with 47 additions and 25 deletions
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2
java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnalyzeAnnotationsWalker.java → java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnalyzeAnnotationsWalker.java
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@ -23,7 +23,7 @@
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.playground.gatk.walkers.variantoptimizer;
package org.broadinstitute.sting.gatk.walkers.analyzeannotations;
import org.broad.tribble.util.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnnotationDataManager.java → java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnnotationDataManager.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.variantoptimizer;
package org.broadinstitute.sting.gatk.walkers.analyzeannotations;
import org.broad.tribble.util.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.BaseUtils;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnnotationDatum.java → java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnnotationDatum.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.variantoptimizer;
package org.broadinstitute.sting.gatk.walkers.analyzeannotations;
import org.broadinstitute.sting.utils.StingException;

7
java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
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@ -47,11 +47,8 @@ import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotationType;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.playground.gatk.walkers.annotator.GenomicAnnotation;
import org.broadinstitute.sting.playground.gatk.walkers.annotator.JoinTable;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
import org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator.*;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.classloader.PackageUtils;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/AminoAcid.java → java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/AminoAcid.java
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@ -23,7 +23,7 @@
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.playground.gatk.walkers.annotator;
package org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator;
/**
* Represents a single amino acid.

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/AminoAcidTable.java → java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/AminoAcidTable.java
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@ -23,7 +23,7 @@
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.playground.gatk.walkers.annotator;
package org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator;
import java.util.HashMap;

12
java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotation.java → java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotation.java
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@ -23,7 +23,7 @@
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.playground.gatk.walkers.annotator;
package org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator;
import java.util.*;
import java.util.Map.Entry;
@ -159,7 +159,7 @@ public class GenomicAnnotation implements InfoFieldAnnotation {
boolean matchFound = false;
for(String hapAlt : hapAltValue.split("[,\\\\/:|]")) {
if(!positiveStrand) {
hapAlt = BaseUtils.simpleReverseComplement(hapAlt);
hapAlt = new String(BaseUtils.simpleReverseComplement(hapAlt.getBytes()));
}
if(!hapAlt.isEmpty() && vcAlt.basesMatch(hapAlt)) {
@ -228,9 +228,9 @@ public class GenomicAnnotation implements InfoFieldAnnotation {
/**
* Combines the 2 values into a full key.
* @param rodBindingName
* @param columnName
* @return
* @param rodBindingName -B name
* @param columnName column name
* @return info field key
*/
public static String generateInfoFieldKey(String rodBindingName, String columnName ) {
return rodBindingName + '.' + columnName;
@ -241,7 +241,7 @@ public class GenomicAnnotation implements InfoFieldAnnotation {
/**
* Replaces any characters that are not allowed in the info field of a VCF file.
*
* @param value
* @param value info field value
* @return the value with any illegal characters replaced by legal ones.
*/
private static String scrubInfoFieldValue(String value) {

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotator.java → java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotator.java
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@ -24,7 +24,7 @@
*/
package org.broadinstitute.sting.playground.gatk.walkers.annotator;
package org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator;
import java.io.IOException;
import java.util.*;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/JoinTable.java → java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTable.java
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@ -23,7 +23,7 @@
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.playground.gatk.walkers.annotator;
package org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator;
import java.io.BufferedReader;
import java.io.FileReader;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/JoinTableParser.java → java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTableParser.java
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@ -23,7 +23,7 @@
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.playground.gatk.walkers.annotator;
package org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator;
import java.io.BufferedReader;
import java.io.IOException;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/TranscriptToInfo.java → java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/TranscriptToInfo.java
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@ -23,7 +23,7 @@
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.playground.gatk.walkers.annotator;
package org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator;
import java.io.*;
import java.util.ArrayList;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java → java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java
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@ -23,7 +23,7 @@
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.playground.gatk.walkers;
package org.broadinstitute.sting.gatk.walkers.beagle;
import org.broad.tribble.util.variantcontext.Allele;
import org.broad.tribble.util.variantcontext.Genotype;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/ProduceBeagleInputWalker.java → java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java
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@ -23,7 +23,7 @@
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.playground.gatk.walkers;
package org.broadinstitute.sting.gatk.walkers.beagle;
import org.broad.tribble.util.variantcontext.Allele;
import org.broad.tribble.util.variantcontext.Genotype;

27
java/test/org/broadinstitute/sting/playground/gatk/walkers/ClipReadsWalkersIntegrationTest.java → java/test/org/broadinstitute/sting/gatk/walkers/ClipReadsWalkersIntegrationTest.java
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@ -1,4 +1,29 @@
package org.broadinstitute.sting.playground.gatk.walkers;
/*
* Copyright (c) 2010.
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.walkers;
import org.broadinstitute.sting.WalkerTest;
import org.junit.Test;

2
java/test/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotatorIntegrationTest.java → java/test/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotatorIntegrationTest.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.annotator;
package org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator;
import java.util.Arrays;

2
java/test/org/broadinstitute/sting/playground/gatk/walkers/BeagleIntegrationTest.java → java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java
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@ -23,7 +23,7 @@
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.playground.gatk.walkers;
package org.broadinstitute.sting.gatk.walkers.beagle;
import org.broadinstitute.sting.WalkerTest;
import org.junit.Test;