BuildBamIndex.java

/*
 * The MIT License
 *
 * 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 picard.sam;

import htsjdk.samtools.BAMIndex;
import htsjdk.samtools.BAMIndexer;
import htsjdk.samtools.BamFileIoUtils;
import htsjdk.samtools.SAMException;
import htsjdk.samtools.SAMFileHeader;
import htsjdk.samtools.SamInputResource;
import htsjdk.samtools.SamReader;
import htsjdk.samtools.SamReaderFactory;
import htsjdk.samtools.util.CloserUtil;
import htsjdk.samtools.util.IOUtil;
import htsjdk.samtools.util.Log;
import picard.cmdline.CommandLineProgram;
import picard.cmdline.CommandLineProgramProperties;
import picard.cmdline.Option;
import picard.cmdline.StandardOptionDefinitions;
import picard.cmdline.programgroups.SamOrBam;

import java.io.File;
import java.net.URL;

/**
 * Command line program to generate a BAM index (.bai) file from a BAM (.bam) file
 *
 * @author Martha Borkan
 */
@CommandLineProgramProperties(
        usage = BuildBamIndex.USAGE_SUMMARY + BuildBamIndex.USAGE_DETAILS,
        usageShort = BuildBamIndex.USAGE_SUMMARY,
        programGroup = SamOrBam.class
)
public class BuildBamIndex extends CommandLineProgram {
    static final String USAGE_SUMMARY = "Generates a BAM index \".bai\" file.  ";
    static final String USAGE_DETAILS = "This tool creates an index file for the input BAM that allows fast look-up of data in a " +
            "BAM file, lke an index on a database. Note that this tool cannot be run on SAM files, and that the input BAM file must be " +
            "sorted in coordinate order." +
            "<h4>Usage example:</h4>" +
            "<pre>" +
            "java -jar picard.jar BuildBamIndex \\<br />" +
            "      I=input.bam" +
            "</pre>" +
            "<hr />";
    private static final Log log = Log.getInstance(BuildBamIndex.class);

    @Option(shortName = StandardOptionDefinitions.INPUT_SHORT_NAME,
            doc = "A BAM file or GA4GH URL to process. Must be sorted in coordinate order.")
    public String INPUT;

    URL inputUrl = null;   // INPUT as URL
    File inputFile = null; // INPUT as File, if it can't be interpreted as a valid URL

    @Option(shortName = StandardOptionDefinitions.OUTPUT_SHORT_NAME,
            doc = "The BAM index file. Defaults to x.bai if INPUT is x.bam, otherwise INPUT.bai.\n" +
                    "If INPUT is a URL and OUTPUT is unspecified, defaults to a file in the current directory.", optional = true)
    public File OUTPUT;

    /** Stock main method for a command line program. */
    public static void main(final String[] argv) {
        System.exit(new BuildBamIndex().instanceMain(argv));
    }

    /**
     * Main method for the program.  Checks that all input files are present and
     * readable and that the output file can be written to.  Then iterates through
     * all the records generating a BAM Index, then writes the bai file.
     */
    protected int doWork() {

        try {
            inputUrl = new URL(INPUT);
        } catch (java.net.MalformedURLException e) {
            inputFile = new File(INPUT);
        }

        // set default output file - input-file.bai
        if (OUTPUT == null) {

            final String baseFileName;
            if (inputUrl != null) {
                final String path = inputUrl.getPath();
                final int lastSlash = path.lastIndexOf('/');
                baseFileName = path.substring(lastSlash + 1, path.length());
            } else {
                baseFileName = inputFile.getAbsolutePath();
            }

            if (baseFileName.endsWith(BamFileIoUtils.BAM_FILE_EXTENSION)) {

                final int index = baseFileName.lastIndexOf('.');
                OUTPUT = new File(baseFileName.substring(0, index) + BAMIndex.BAMIndexSuffix);

            } else {
                OUTPUT = new File(baseFileName + BAMIndex.BAMIndexSuffix);
            }
        }

        IOUtil.assertFileIsWritable(OUTPUT);
        final SamReader bam;

        if (inputUrl != null) {
            // remote input
            bam = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE)
                    .disable(SamReaderFactory.Option.EAGERLY_DECODE)
                    .enable(SamReaderFactory.Option.INCLUDE_SOURCE_IN_RECORDS)
                    .open(SamInputResource.of(inputUrl));
        } else {
            // input from a normal file
            IOUtil.assertFileIsReadable(inputFile);
            bam = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE)
                    .enable(SamReaderFactory.Option.INCLUDE_SOURCE_IN_RECORDS)
                    .open(inputFile);
        }

        if (bam.type() != SamReader.Type.BAM_TYPE) {
            throw new SAMException("Input file must be bam file, not sam file.");
        }

        if (!bam.getFileHeader().getSortOrder().equals(SAMFileHeader.SortOrder.coordinate)) {
            throw new SAMException("Input bam file must be sorted by coordinate");
        }

        BAMIndexer.createIndex(bam, OUTPUT);

        log.info("Successfully wrote bam index file " + OUTPUT);
        CloserUtil.close(bam);
        return 0;
    }
}