picard.sam.BamIndexStats Maven / Gradle / Ivy
/*
* 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.BAMIndexMetaData;
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;
/**
* Command line program to print statistics from BAM index (.bai) file
* Statistics include count of aligned and unaligned reads for each reference sequence
* and a count of all records with no start coordinate.
* Similar to the 'samtools idxstats' command.
*
* @author Martha Borkan
*/
@CommandLineProgramProperties(
usage = BamIndexStats.USAGE_SUMMARY + BamIndexStats.USAGE_DETAILS,
usageShort = BamIndexStats.USAGE_SUMMARY,
programGroup = SamOrBam.class
)
public class BamIndexStats extends CommandLineProgram {
static final String USAGE_SUMMARY = "Generate index statistics from a BAM file";
static final String USAGE_DETAILS = "This tool calculates statistics from a BAM index (.bai) file, emulating the behavior of the " +
"\"samtools idxstats\" command. The statistics collected include counts of aligned and unaligned reads as well as all " +
"records with no start coordinate. The input to the tool is the BAM file name but it must be accompanied by a corresponding " +
"index file.
" +
"Usage example:
" +
"" +
"java -jar picard.jar BamIndexStats \\
" +
" I=input.bam \\
" +
" O=output" +
"" +
"
" ;
private static final Log log = Log.getInstance(BamIndexStats.class);
@Option(shortName= StandardOptionDefinitions.INPUT_SHORT_NAME,
doc="A BAM file to process.")
public File INPUT;
/** Stock main method for a command line program. */
public static void main(final String[] argv) {
System.exit(new BamIndexStats().instanceMain(argv));
}
/**
* Main method for the program. Checks that input file is present and
* readable, then iterates through the index printing meta data to stdout.
*/
protected int doWork() {
if (INPUT.getName().endsWith(BAMIndex.BAMIndexSuffix))
log.warn("INPUT should be the BAM file name, not its index file");
IOUtil.assertFileIsReadable(INPUT);
BAMIndexMetaData.printIndexStats(INPUT);
return 0;
}
}