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Moved AnnotatorInputTableFeature and Codec to org.broadinstitute.sting.gatk.refdata.features.annotator 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3426 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
weisburd 2010-05-24 14:38:07 +00:00
parent aca3bcb193
commit 4aa749c709
1 changed files with 27 additions and 3 deletions
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30
java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/TranscriptToInfo.java
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@ -1,3 +1,28 @@
/*
* Copyright (c) 2010 The Broad Institute
*
* 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.playground.gatk.walkers.annotator;
import java.io.BufferedWriter;
@ -21,8 +46,8 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.features.sampileup.AnnotatorInputTableCodec;
import org.broadinstitute.sting.gatk.refdata.features.sampileup.AnnotatorInputTableFeature;
import org.broadinstitute.sting.gatk.refdata.features.annotator.AnnotatorInputTableCodec;
import org.broadinstitute.sting.gatk.refdata.features.annotator.AnnotatorInputTableFeature;
import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
import org.broadinstitute.sting.gatk.walkers.By;
import org.broadinstitute.sting.gatk.walkers.DataSource;
@ -33,7 +58,6 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.gatk.walkers.TreeReducible;
import org.broadinstitute.sting.gatk.walkers.Window;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.StingException;