Package org.snpeff.snpEffect.commandLine

Class SnpEffCmdCds

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_PERCENTAGE
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(java.lang.String genomeVer, java.lang.String configFile, java.lang.String cdsFile)
SnpEffCmdCds(Config config)

Method Summary

Modifier and Type	Method	Description
void	parseArgs(java.lang.String[] args)	Parse command line arguments
boolean	run()	Run command
void	setCheckNumOk(boolean checkNumOk)
void	setStoreAlignments(boolean storeAlignments)
void	usage(java.lang.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 Detail

onlyOneError

public static boolean onlyOneError

MAX_ERROR_PERCENTAGE

public static double MAX_ERROR_PERCENTAGE

MAX_ALIGN_LENGTH

public static int MAX_ALIGN_LENGTH

Constructor Detail

SnpEffCmdCds

public SnpEffCmdCds()

SnpEffCmdCds

public SnpEffCmdCds(Config config)

SnpEffCmdCds

public SnpEffCmdCds(java.lang.String genomeVer,
                    java.lang.String configFile,
                    java.lang.String cdsFile)

Method Detail

parseArgs

public void parseArgs(java.lang.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)

setStoreAlignments

public void setStoreAlignments(boolean storeAlignments)

usage

public void usage(java.lang.String message)

Show usage and exit

Specified by:

usage in interface CommandLine

Overrides:

usage in class SnpEff