75 lines
2.7 KiB
Java
75 lines
2.7 KiB
Java
package org.broadinstitute.sting.playground.somaticcoverage;
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import org.broadinstitute.sting.gatk.CommandLineExecutable;
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import org.broadinstitute.sting.gatk.GATKArgumentCollection;
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import org.broadinstitute.sting.utils.cmdLine.Argument;
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import java.io.File;
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import java.util.List;
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import java.util.ArrayList;
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/*
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* Copyright (c) 2009 The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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/**
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* @author aaron
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*
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*
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* a executable command line for the Somatic Coverage Walker.
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*/
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public class SomaticCoverageTool extends CommandLineExecutable {
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// the two sam/bam files, one for cancer, one for normal
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@Argument(fullName = "bam_file", shortName = "I", doc = "The bam files, one for the tumor one for the normal", required = true)
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public List<File> samFiles = new ArrayList<File>();
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/** Required main method implementation. */
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public static void main( String[] argv ) {
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try {
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SomaticCoverageTool instance = new SomaticCoverageTool();
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start(instance, argv);
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} catch (Exception e) {
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exitSystemWithError(e);
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}
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}
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/**
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* a required method, returns the analysis name. This is usually the walker
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* name with 'Walker' stripped off.
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*
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* @return the name of the analysis we're running
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*/
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protected String getAnalysisName() {
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return "SomaticCoverage";
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}
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/** override any arguments we see fit. */
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protected GATKArgumentCollection getArgumentCollection() {
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GATKArgumentCollection argCollection = GATKArgumentCollection.unmarshal(getClass().getClassLoader().getResourceAsStream("SomaticCoverage.xml"));
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argCollection.samFiles = samFiles;
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return argCollection;
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}
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}
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