Package org.snpeff.snpEffect.commandLine

Class SnpEffCmdCount

java.lang.Object

org.snpeff.SnpEff

org.snpeff.snpEffect.commandLine.SnpEffCmdCount

All Implemented Interfaces:

CommandLine

public class SnpEffCmdCount
extends SnpEff

Count reads from a BAM file given a list of intervals

Author:

pablocingolani

Nested Class Summary

Nested classes/interfaces inherited from class org.snpeff.SnpEff

SnpEff.GeneDatabaseFormat, SnpEff.InputFormat, SnpEff.OutputFormat

Field Summary

Fields inherited from class org.snpeff.SnpEff

args, BUILD, BUILD_DATE, canonical, canonicalFile, command, COMMAND_LINE_WIDTH, config, configFile, configOverride, customIntervalFiles, dataDir, debug, DEFAULT_COMMAND, download, expandIub, filterIntervalFiles, genome, genomeVer, help, hgvs, hgvsForce, hgvsOld, hgvsOneLetterAa, hgvsShift, hgvsTrId, interaction, log, maxTranscriptSupportLevel, motif, multiThreaded, nextProt, nextProtKeepAllTrs, noGenome, numWorkers, onlyProtein, onlyRegulation, onlyTranscriptsFile, output, quiet, regulationTracks, REVISION, saveOutput, shiftArgs, snpEffCmd, SOFTWARE_NAME, spliceRegionExonSize, spliceRegionIntronMax, spliceRegionIntronMin, spliceSiteSize, strict, suppressOutput, treatAllAsProteinCoding, upDownStreamLength, verbose, VERSION, VERSION_AUTHOR, VERSION_BUILD, VERSION_MAJOR, VERSION_SHORT

Constructor Summary

Constructors

Constructor	Description
SnpEffCmdCount()

Method Summary

Modifier and Type	Method	Description
void	parseArgs(java.lang.String[] args)	Parse
boolean	run()	Run
void	usage(java.lang.String message)	Show 'usage' message and exit with an error code '-1'

Methods inherited from class org.snpeff.SnpEff

addRegulationTrack, canonical, cmd, commandLineStr, getArgs, getConfig, getConfigFile, getOutput, isOpt, load, loadConfig, loadCustomFile, loadDb, loadMarkers, main, reportValues, run, setCanonical, setConfig, setConfigFile, setDebug, setGenomeVer, setLog, setNextProt, setNextProtKeepAllTrs, setShiftHgvs, setSpliceSiteSize, setSupressOutput, setUpDownStreamLength, setVerbose, usageDb, usageGeneric, usageGenericAndDb

Methods inherited from class java.lang.Object

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

Constructor Detail

SnpEffCmdCount

public SnpEffCmdCount()

Method Detail

parseArgs

public void parseArgs(java.lang.String[] args)

Parse

Specified by:

parseArgs in interface CommandLine

Overrides:

parseArgs in class SnpEff

Parameters:

args -

run

public boolean run()

Run

Specified by:

run in interface CommandLine

Overrides:

run in class SnpEff

usage

public void usage(java.lang.String message)

Description copied from class: SnpEff

Show 'usage' message and exit with an error code '-1'

Specified by:

usage in interface CommandLine

Overrides:

usage in class SnpEff