picard.sam

Class BuildBamIndex

java.lang.Object

picard.cmdline.CommandLineProgram

picard.sam.BuildBamIndex

public class BuildBamIndex
extends CommandLineProgram

Command line program to generate a BAM index (.bai) file from a BAM (.bam) file

Author:

Martha Borkan

Field Summary

Fields

Modifier and Type	Field and Description
java.lang.String	INPUT
java.io.File	OUTPUT

Fields inherited from class picard.cmdline.CommandLineProgram

COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, TMP_DIR, VALIDATION_STRINGENCY, VERBOSITY

Constructor Summary

Constructors

Constructor and Description
BuildBamIndex()

Method Summary

Modifier and Type	Method and Description
protected int	doWork() Main method for the program.
static void	main(java.lang.String[] argv) Stock main method for a command line program.

Methods inherited from class picard.cmdline.CommandLineProgram

customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

INPUT

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

OUTPUT

@Option(shortName="O",
        doc="The BAM index file. Defaults to x.bai if INPUT is x.bam, otherwise INPUT.bai.\nIf INPUT is a URL and OUTPUT is unspecified, defaults to a file in the current directory.",
        optional=true)
public java.io.File OUTPUT

Constructor Detail

BuildBamIndex

public BuildBamIndex()

Method Detail

main

public static void main(java.lang.String[] argv)

Stock main method for a command line program.

doWork

protected int doWork()

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.

Specified by:

doWork in class CommandLineProgram

Returns:

program exit status.