diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/TranscriptToInfo.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/TranscriptToInfo.java index 25be52a7d..29a42d5ea 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/TranscriptToInfo.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/TranscriptToInfo.java @@ -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;