/*
* 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;
}
}