de.helmholtz_muenchen.ibis.ngs.vcfmerger.VCFMerger.java Source code

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Here is the source code for de.helmholtz_muenchen.ibis.ngs.vcfmerger.VCFMerger.java

Source

/**
 *  Copyright (C) 2016 the Knime4NGS contributors.
 *  Website: http://ibisngs.github.io/knime4ngs
 *  
 *  This file is part of the KNIME4NGS KNIME extension.
 *  
 *  The KNIME4NGS extension is free software: you can redistribute it and/or modify
 *  it under the terms of the GNU General Public License as published by
 *  the Free Software Foundation, either version 3 of the License, or
 *  (at your option) any later version.
 *  
 *  This program is distributed in the hope that it will be useful,
 *  but WITHOUT ANY WARRANTY; without even the implied warranty of
 *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *  GNU General Public License for more details.
 *  
 *  You should have received a copy of the GNU General Public License
 *  along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */
package de.helmholtz_muenchen.ibis.ngs.vcfmerger;

import java.util.ArrayList;
import java.util.LinkedList;
import java.util.concurrent.ExecutionException;

import org.apache.commons.lang3.StringUtils;
import org.knime.core.node.CanceledExecutionException;
import org.knime.core.node.ExecutionContext;
import org.knime.core.node.InvalidSettingsException;
import org.knime.core.node.NodeLogger;

import de.helmholtz_muenchen.ibis.utils.threads.Executor;
import de.helmholtz_muenchen.ibis.utils.threads.UnsuccessfulExecutionException;

/**
 * 
 * @author Maximilian Hastreiter
 *
 */

public class VCFMerger {

    public static String mergeVCFs(String GATK, String RefGenome, String Infolder, String Outfolder, String Regex,
            String GenotypeMergeOption, final ExecutionContext exec, NodeLogger logger, String OUTFILETAG)
            throws InvalidSettingsException {

        LinkedList<String> Files2Merge = new LinkedList<String>();
        de.helmholtz_muenchen.ibis.utils.ngs.FileSearch.searchWithV(Infolder, Regex, Files2Merge);
        String OUTFILE = merge_vcfs(GATK, RefGenome, Files2Merge, Outfolder, GenotypeMergeOption, exec, logger,
                OUTFILETAG);
        return OUTFILE;
    }

    /**
     * Executes vcf-merge 
     * @param Files2Merge
     * @param Outfolder
     * @param exec
     * @param logger
     */
    private static String merge_vcfs(String GATK, String RefGenome, LinkedList<String> Files2Merge,
            String Outfolder, String GenotypeMergeOption, ExecutionContext exec, NodeLogger logger,
            String OUTFILETAG) {
        ArrayList<String> command = new ArrayList<String>();

        String OUTFILE = Outfolder + "/AllSamples_vcfmerger" + OUTFILETAG + ".vcf";
        String ERRFILE = Outfolder + "/AllSamples_vcfmerger" + OUTFILETAG + ".vcf.err";

        command.add("java");
        command.add("-jar " + GATK);
        command.add("-T CombineVariants");
        command.add("-R " + RefGenome);
        command.addAll(Files2Merge);
        command.add("--genotypemergeoption " + GenotypeMergeOption);
        command.add("-o " + OUTFILE);

        try {
            Executor.executeCommand(new String[] { StringUtils.join(command, " ") }, exec, new String[] {}, logger,
                    OUTFILE, ERRFILE);

        } catch (CanceledExecutionException | InterruptedException | ExecutionException
                | UnsuccessfulExecutionException e) {
            e.printStackTrace();
        }
        return OUTFILE;
    }

}