java.lang.Object

org.snpeff.SnpEff

org.snpeff.snpEffect.commandLine.SnpEffCmdCds

All Implemented Interfaces:: CommandLine

public class SnpEffCmdCds extends SnpEff

Command line: Calculate coding sequences from a file and compare them to the ones calculated from our data structures

Note: This is done in order to see potential incompatibility errors between genome sequence and annotation.

Author:: pcingola

Nested Class Summary

Nested classes/interfaces inherited from class org.snpeff.SnpEff
SnpEff.GeneDatabaseFormat, SnpEff.InputFormat, SnpEff.OutputFormat
Field Summary

Fields

Modifier and Type

Field

Description

static int

MAX_ALIGN_LENGTH

static double

MAX_ERROR_RATE

static boolean

onlyOneError

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

SnpEffCmdCds()

SnpEffCmdCds(String genomeVer, String configFile, String cdsFile)

SnpEffCmdCds(Config config)
Method Summary

Modifier and Type

Method

Description

void

parseArgs(String[] args)

Parse command line arguments

boolean

run()

Run command

void

setCheckNumOk(boolean checkNumOk)

void

setMaxErrorRate(double maxErrorRate)

void

setStoreAlignments(boolean storeAlignments)

void

usage(String message)

Show usage and exit

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

Field Details
- onlyOneError
  
  public static boolean onlyOneError
- MAX_ERROR_RATE
  
  public static double MAX_ERROR_RATE
- MAX_ALIGN_LENGTH
  
  public static int MAX_ALIGN_LENGTH
Constructor Details
- SnpEffCmdCds
  
  public SnpEffCmdCds()
- SnpEffCmdCds
  
  public SnpEffCmdCds(Config config)
- SnpEffCmdCds
  
  public SnpEffCmdCds(String genomeVer, String configFile, String cdsFile)
Method Details
- parseArgs
  
  public void parseArgs(String[] args)
  
  Parse command line arguments
  
  Specified by:
  
  parseArgs in interface CommandLine
  
  Overrides:
  
  parseArgs in class SnpEff
- run
  
  public boolean run()
  
  Run command
  
  Specified by:
  
  run in interface CommandLine
  
  Overrides:
  
  run in class SnpEff
- setCheckNumOk
  
  public void setCheckNumOk(boolean checkNumOk)
- setMaxErrorRate
  
  public void setMaxErrorRate(double maxErrorRate)
- setStoreAlignments
  
  public void setStoreAlignments(boolean storeAlignments)
- usage
  
  public void usage(String message)
  
  Show usage and exit
  
  Specified by:
  
  usage in interface CommandLine
  
  Overrides:
  
  usage in class SnpEff

Class SnpEffCmdCds

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

Field Details

onlyOneError

MAX_ERROR_RATE

MAX_ALIGN_LENGTH

Constructor Details

SnpEffCmdCds

SnpEffCmdCds

SnpEffCmdCds

Method Details

parseArgs

run

setCheckNumOk

setMaxErrorRate

setStoreAlignments

usage