picard.sam

Class BamIndexStats

java.lang.Object

picard.cmdline.CommandLineProgram

picard.sam.BamIndexStats

public class BamIndexStats
extends CommandLineProgram

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

Field Summary

Fields

Modifier and Type	Field and Description
java.io.File	INPUT

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
BamIndexStats()

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 to process.")
public java.io.File INPUT

Constructor Detail

BamIndexStats

public BamIndexStats()

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 input file is present and readable, then iterates through the index printing meta data to stdout.

Specified by:

doWork in class CommandLineProgram

Returns:

program exit status.