com.cloudera.science.quince.PrintSamplesTool.java Source code

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Here is the source code for com.cloudera.science.quince.PrintSamplesTool.java

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/*
 * Copyright (c) 2015, Cloudera, Inc. All Rights Reserved.
 *
 * Cloudera, Inc. licenses this file to you under the Apache License,
 * Version 2.0 (the "License"). You may not use this file except in
 * compliance with the License. You may obtain a copy of the License at
 *
 * http://www.apache.org/licenses/LICENSE-2.0
 *
 * This software is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR
 * CONDITIONS OF ANY KIND, either express or implied. See the License for
 * the specific language governing permissions and limitations under the
 * License.
 */

package com.cloudera.science.quince;

import com.beust.jcommander.JCommander;
import com.beust.jcommander.Parameter;
import com.beust.jcommander.ParameterException;
import com.beust.jcommander.Parameters;
import com.google.common.base.Joiner;
import com.google.common.collect.Iterables;
import java.util.List;
import java.util.Set;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.conf.Configured;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.util.Tool;
import org.apache.hadoop.util.ToolRunner;

/**
 * Prints the unique sample IDs stored in VCF files.
 */
@Parameters(commandDescription = "Print samples tool")
public class PrintSamplesTool extends Configured implements Tool {

    @Parameter(description = "<input-path>")
    private List<String> paths;

    @Parameter(names = "--samples-per-line")
    private int samplesPerLine = 1;

    @Override
    public int run(String[] args) throws Exception {
        JCommander jc = new JCommander(this);
        try {
            jc.parse(args);
        } catch (ParameterException e) {
            jc.usage();
            return 1;
        }

        if (paths == null || paths.size() != 1) {
            jc.usage();
            return 1;
        }

        String inputPathString = paths.get(0);

        Configuration conf = getConf();
        Path inputPath = new Path(inputPathString);

        Path[] vcfs = FileUtils.findVcfs(inputPath, conf);
        Set<String> samples = SampleUtils.uniqueSamples(conf, vcfs);

        if (samplesPerLine == 0) { // all on one line
            System.out.println(Joiner.on(',').join(samples));
        } else {
            for (List<String> line : Iterables.partition(samples, samplesPerLine)) {
                System.out.println(Joiner.on(',').join(line));
            }
        }

        return 0;
    }

    public static void main(String[] args) throws Exception {
        int exitCode = ToolRunner.run(new PrintSamplesTool(), args);
        System.exit(exitCode);
    }

}