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, tags, tagsNo, 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(String[] args)

Parse

boolean

run()

Run

void

usage(String message)

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

Methods inherited from class org.snpeff.SnpEff
addRegulationTrack, canonical, cmd, commandLineStr, filterTags, 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 Details
- SnpEffCmdCount
  
  public SnpEffCmdCount()
Method Details
- parseArgs
  
  public void parseArgs(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(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

Class SnpEffCmdCount

Nested Class Summary

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

Field Summary

Fields inherited from class org.snpeff.SnpEff

Constructor Summary

Method Summary

Methods inherited from class org.snpeff.SnpEff

Methods inherited from class java.lang.Object

Constructor Details

SnpEffCmdCount

Method Details

parseArgs

run

usage