com.github.lindenb.jvarkit.tools.misc.AddLinearIndexToBed.java Source code

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Here is the source code for com.github.lindenb.jvarkit.tools.misc.AddLinearIndexToBed.java

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/*
The MIT License (MIT)
    
Copyright (c) 2015 Pierre Lindenbaum
    
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 com.github.lindenb.jvarkit.tools.misc;

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.PrintStream;
import java.util.Arrays;
import java.util.Collection;
import java.util.List;
import java.util.regex.Pattern;
import htsjdk.samtools.SAMSequenceDictionary;
import htsjdk.samtools.SAMSequenceRecord;
import htsjdk.samtools.util.CloserUtil;
import com.github.lindenb.jvarkit.io.IOUtils;
import com.github.lindenb.jvarkit.util.picard.SAMSequenceDictionaryFactory;

public class AddLinearIndexToBed extends AbstractAddLinearIndexToBed {
    private static final org.apache.commons.logging.Log LOG = org.apache.commons.logging.LogFactory
            .getLog(AddLinearIndexToBed.class);

    public AddLinearIndexToBed() {

    }

    private SAMSequenceDictionary dictionary = null;
    private long tid2offset[] = null;

    protected int doWork(InputStream is, PrintStream out) throws IOException {
        final Pattern tab = Pattern.compile("[\t]");
        BufferedReader in = new BufferedReader(new InputStreamReader(is));
        String line = null;
        while ((line = in.readLine()) != null) {
            if (line.isEmpty() || line.startsWith("#") || line.startsWith("track") || line.startsWith("browser"))
                continue;
            String tokens[] = tab.split(line, 3);
            if (tokens.length < 2) {
                LOG.warn("Bad chrom/pos line:" + line);
                continue;
            }
            SAMSequenceRecord ssr = this.dictionary.getSequence(tokens[0]);
            if (ssr == null) {
                for (SAMSequenceRecord sr2 : this.dictionary.getSequences()) {
                    LOG.info("available " + sr2.getSequenceName());
                }
                throw new IOException("undefined chromosome:" + tokens[0]);
            }
            int pos0 = Integer.parseInt(tokens[1]);
            if (pos0 < 0 || pos0 >= ssr.getSequenceLength()) {
                LOG.warn("position is out of range for : " + line + " length(" + tokens[0] + ")="
                        + ssr.getSequenceLength());
            }
            out.print(this.tid2offset[ssr.getSequenceIndex()] + pos0);
            out.print('\t');
            out.print(line);
            out.println();
            if (out.checkError())
                break;
        }
        return 0;
    }

    @Override
    public Collection<Throwable> call() throws Exception {
        if (refFile == null) {
            return wrapException("Reference file undefined");
        }
        PrintStream out = null;
        try {

            final List<String> args = this.getInputFiles();
            this.dictionary = new SAMSequenceDictionaryFactory().load(refFile);
            this.tid2offset = new long[this.dictionary.size()];
            Arrays.fill(this.tid2offset, 0L);
            for (int i = 1; i < this.dictionary.size(); ++i) {
                this.tid2offset[i] = this.tid2offset[i - 1]
                        + this.dictionary.getSequence(i - 1).getSequenceLength();
            }
            out = openFileOrStdoutAsPrintStream();

            if (args.isEmpty()) {
                LOG.info("reading stdin");
                doWork(stdin(), out);
            } else {
                for (final String arg : args) {
                    LOG.info("opening " + arg);
                    InputStream in = IOUtils.openURIForReading(arg);
                    doWork(in, stdout());
                    CloserUtil.close(out);
                }
            }

            return RETURN_OK;
        } catch (Exception err) {
            return wrapException(err);
        } finally {
            CloserUtil.close(out);
            dictionary = null;
            tid2offset = null;
        }
    }

    /**
     * @param args
     */
    public static void main(String[] args) {
        new AddLinearIndexToBed().instanceMainWithExit(args);
    }
}