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Deprecated 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4623 348d0f76-0448-11de-a6fe-93d51630548a
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ebanks 2010-11-04 02:07:40 +00:00
parent 42e9987e69
commit 87f6738d4c
1 changed files with 0 additions and 84 deletions
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java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/TranscriptToInfo.java
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/*
* 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.gatk.walkers.annotator.genomicannotator;
import java.io.*;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.features.annotator.AnnotatorInputTableFeature;
import org.broadinstitute.sting.gatk.walkers.By;
import org.broadinstitute.sting.gatk.walkers.DataSource;
import org.broadinstitute.sting.gatk.walkers.RMD;
import org.broadinstitute.sting.gatk.walkers.Reference;
import org.broadinstitute.sting.gatk.walkers.Requires;
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.exceptions.UserException;
/**
* Takes a table of transcripts (eg. UCSC refGene, knownGene, and CCDS tables) and generates the big table which contains
* annotations for each possible variant at each transcript position (eg. 4 variants at each genomic position).
*
* Required args:
* -B - specifies the input file (ex. -B transcripts,AnnotatorInputTable,/path/to/transcript_table_file.txt)
* -n - Specifies which column(s) from the transcript table contain the gene name(s). (ex. -n name,name2 (for the UCSC refGene table))
* WARNING: The gene names for each record, when taken together, should provide a unique id for that record relative to all other records in the file.
*
*
* The map & reduce types are both TreeMap<String, String>.
* Each TreeMap entry represents one line in the output file. The TreeMap key is a combination of a given output line's position (so that this key can be used to sort all output lines
* by reference order), as well as allele and gene names (so that its unique across all output lines). The String value is the output line itself.
*/
@Reference(window=@Window(start=-4,stop=4))
@By(DataSource.REFERENCE)
@Requires(value={DataSource.REFERENCE}, referenceMetaData={ @RMD(name="transcripts",type=AnnotatorInputTableFeature.class) } )
public class TranscriptToInfo extends RodWalker<Integer, Integer> implements TreeReducible<Integer>
{
@Output
private PrintWriter out;
@Argument(fullName="unique-gene-name-columns", shortName="n", doc="Specifies which column(s) from the transcript table contains the gene name(s). For example, -B transcripts,AnnotatorInputTable,/data/refGene.txt -n name,name2 specifies that the name and name2 columns are gene names. WARNING: the gene names for each record, when taken together, should provide a unique id for that record relative to all other records in the file. If this is not the case, an error will be thrown. ", required=true)
private String[] GENE_NAME_COLUMNS = {};
public void initialize() {
throw new UserException.MissingWalker("TranscriptToInfo", "This walker is no longer supported. We are actively working on a bug-free replacement. We thank you for your patience at this time.");
}
public Integer reduceInit() { return 0; }
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { return 0; }
public Integer reduce(Integer value, Integer sum) { return 0; }
public Integer treeReduce(Integer lhs, Integer rhs) { return 0; }
}