Package org.snpsift
Class SnpSift
- java.lang.Object
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- org.snpsift.SnpSift
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- All Implemented Interfaces:
org.snpeff.snpEffect.commandLine.CommandLine
,org.snpeff.snpEffect.VcfAnnotator
- Direct Known Subclasses:
SnpSiftCmdAlleleMatrix
,SnpSiftCmdAnnotate
,SnpSiftCmdCaseControl
,SnpSiftCmdCaseControlSummary
,SnpSiftCmdConcordance
,SnpSiftCmdCovarianceMatrix
,SnpSiftCmdDbNsfp
,SnpSiftCmdExtractFields
,SnpSiftCmdFilter
,SnpSiftCmdFilterChrPos
,SnpSiftCmdFilterGt
,SnpSiftCmdGeneSets
,SnpSiftCmdGt
,SnpSiftCmdGwasCatalog
,SnpSiftCmdHwe
,SnpSiftCmdIntersect
,SnpSiftCmdIntervals
,SnpSiftCmdIntervalsIndex
,SnpSiftCmdJoin
,SnpSiftCmdPedShow
,SnpSiftCmdPhastCons
,SnpSiftCmdPrivate
,SnpSiftCmdRemoveReferenceGenotypes
,SnpSiftCmdRmInfo
,SnpSiftCmdSort
,SnpSiftCmdSplit
,SnpSiftCmdTsTv
,SnpSiftCmdVarType
,SnpSiftCmdVcf2Tped
,SnpSiftCmdVcfCheck
,SnpSiftCmdVcfOperator
public class SnpSift extends java.lang.Object implements org.snpeff.snpEffect.VcfAnnotator, org.snpeff.snpEffect.commandLine.CommandLine
Generic SnpSift tool caller- Author:
- pablocingolani
-
-
Field Summary
Fields Modifier and Type Field Description protected java.lang.String[]
args
static java.lang.String
BUILD
protected java.lang.String
command
protected org.snpeff.snpEffect.Config
config
protected java.lang.String
configFile
protected java.lang.String
dataDir
protected java.lang.String
dbFileName
protected boolean
dbTabix
protected java.lang.String
dbType
protected boolean
debug
protected boolean
download
static java.lang.String[]
EMPTY_ARGS
protected java.util.HashMap<java.lang.String,java.lang.Integer>
errCount
protected java.lang.String
genomeVersion
protected boolean
help
protected boolean
log
protected boolean
needsConfig
protected boolean
needsDb
protected boolean
needsGenome
protected int
numWorkers
protected java.lang.StringBuilder
output
protected boolean
quiet
static java.lang.String
REVISION
protected boolean
saveOutput
protected java.lang.String[]
shiftArgs
static int
SHOW_EVERY_VCFLINES
protected boolean
showVcfHeader
protected boolean
showVersion
static java.lang.String
SOFTWARE_NAME
protected boolean
suppressOutput
protected boolean
vcfHeaderAddProgramVersion
protected boolean
vcfHeaderProcessed
protected java.lang.String
vcfInputFile
protected boolean
verbose
static java.lang.String
VERSION
static java.lang.String
VERSION_MAJOR
static java.lang.String
VERSION_NO_NAME
static java.lang.String
VERSION_SHORT
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
addHeaders(org.snpeff.fileIterator.VcfFileIterator vcfFile)
Add VCF headersboolean
annotate(org.snpeff.vcf.VcfEntry vcfEntry)
boolean
annotateFinish(org.snpeff.fileIterator.VcfFileIterator vcfFile)
boolean
annotateInit(org.snpeff.fileIterator.VcfFileIterator vcfFile)
SnpSift
cmd()
Run: Executes the appropriate classprotected java.lang.String
commandLineStr()
Show command lineprotected boolean
databaseDownload()
Download a databaseprotected java.lang.String
databaseFind()
Find database file name.void
error(java.lang.Throwable e, java.lang.String message)
Show an error (if not 'quiet' mode)java.lang.String[]
getArgs()
org.snpeff.snpEffect.Config
getConfig()
java.lang.String
getConfigFile()
java.lang.String
getOutput()
protected java.util.List<org.snpeff.vcf.VcfHeaderEntry>
headers()
Headers to addvoid
init()
Initialize default valuesprotected boolean
isOpt(java.lang.String arg)
Is this a command line option (e.g.protected void
loadConfig()
Read config filestatic void
main(java.lang.String[] args)
Mainprotected org.snpeff.fileIterator.VcfFileIterator
openVcfInputFile()
Open VCF input filevoid
parseArgs(java.lang.String[] args)
Parse command line argumentsprotected java.lang.String
processVcfHeader(org.snpeff.fileIterator.VcfFileIterator vcf)
Process VCF header related issuesboolean
run()
void
setCommand(java.lang.Class clss)
void
setCommand(java.lang.String command)
void
setConfig(org.snpeff.snpEffect.Config config)
void
setConfigFile(java.lang.String configFile)
void
setDbFileName(java.lang.String dbFileName)
void
setDebug(boolean debug)
void
setQuiet(boolean quiet)
void
setSaveOutput(boolean saveOutput)
void
setShowVcfHeader(boolean showVcfHeader)
void
setShowVersion(boolean showVersion)
void
setSuppressOutput(boolean suppressOutput)
void
setVcfHeaderAddProgramVersion(boolean vcfHeaderAddProgramVersion)
void
setVerbose(boolean verbose)
void
showCmd()
Show command linevoid
showVersion()
Show version numberjava.lang.String
unSanitize(java.lang.String str)
Convert a sanitized expression (from Galaxy) back to the original string References: http://www.mail-archive.com/galaxy-dev@lists.bx.psu.edu/msg00530.htmlvoid
usage(java.lang.String msg)
Show usage messageprotected void
usageGenericAndDb()
Options common to all commands
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-
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Field Detail
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BUILD
public static final java.lang.String BUILD
- See Also:
- Constant Field Values
-
SOFTWARE_NAME
public static final java.lang.String SOFTWARE_NAME
- See Also:
- Constant Field Values
-
VERSION_MAJOR
public static final java.lang.String VERSION_MAJOR
- See Also:
- Constant Field Values
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REVISION
public static final java.lang.String REVISION
- See Also:
- Constant Field Values
-
VERSION_SHORT
public static final java.lang.String VERSION_SHORT
- See Also:
- Constant Field Values
-
VERSION
public static final java.lang.String VERSION
- See Also:
- Constant Field Values
-
VERSION_NO_NAME
public static final java.lang.String VERSION_NO_NAME
- See Also:
- Constant Field Values
-
SHOW_EVERY_VCFLINES
public static int SHOW_EVERY_VCFLINES
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EMPTY_ARGS
public static final java.lang.String[] EMPTY_ARGS
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dbTabix
protected boolean dbTabix
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debug
protected boolean debug
-
download
protected boolean download
-
help
protected boolean help
-
log
protected boolean log
-
needsConfig
protected boolean needsConfig
-
needsDb
protected boolean needsDb
-
needsGenome
protected boolean needsGenome
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quiet
protected boolean quiet
-
saveOutput
protected boolean saveOutput
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showVcfHeader
protected boolean showVcfHeader
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showVersion
protected boolean showVersion
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suppressOutput
protected boolean suppressOutput
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vcfHeaderProcessed
protected boolean vcfHeaderProcessed
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vcfHeaderAddProgramVersion
protected boolean vcfHeaderAddProgramVersion
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verbose
protected boolean verbose
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args
protected java.lang.String[] args
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command
protected java.lang.String command
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dbFileName
protected java.lang.String dbFileName
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dbType
protected java.lang.String dbType
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genomeVersion
protected java.lang.String genomeVersion
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vcfInputFile
protected java.lang.String vcfInputFile
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numWorkers
protected int numWorkers
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output
protected java.lang.StringBuilder output
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errCount
protected java.util.HashMap<java.lang.String,java.lang.Integer> errCount
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config
protected org.snpeff.snpEffect.Config config
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configFile
protected java.lang.String configFile
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dataDir
protected java.lang.String dataDir
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shiftArgs
protected java.lang.String[] shiftArgs
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Method Detail
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main
public static void main(java.lang.String[] args)
Main
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addHeaders
public boolean addHeaders(org.snpeff.fileIterator.VcfFileIterator vcfFile)
Add VCF headers- Specified by:
addHeaders
in interfaceorg.snpeff.snpEffect.VcfAnnotator
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annotate
public boolean annotate(org.snpeff.vcf.VcfEntry vcfEntry)
- Specified by:
annotate
in interfaceorg.snpeff.snpEffect.VcfAnnotator
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annotateFinish
public boolean annotateFinish(org.snpeff.fileIterator.VcfFileIterator vcfFile)
- Specified by:
annotateFinish
in interfaceorg.snpeff.snpEffect.VcfAnnotator
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annotateInit
public boolean annotateInit(org.snpeff.fileIterator.VcfFileIterator vcfFile)
- Specified by:
annotateInit
in interfaceorg.snpeff.snpEffect.VcfAnnotator
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cmd
public SnpSift cmd()
Run: Executes the appropriate class
-
commandLineStr
protected java.lang.String commandLineStr()
Show command line
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databaseDownload
protected boolean databaseDownload()
Download a database
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databaseFind
protected java.lang.String databaseFind()
Find database file name.
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error
public void error(java.lang.Throwable e, java.lang.String message)
Show an error (if not 'quiet' mode)
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getArgs
public java.lang.String[] getArgs()
- Specified by:
getArgs
in interfaceorg.snpeff.snpEffect.commandLine.CommandLine
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getConfig
public org.snpeff.snpEffect.Config getConfig()
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getConfigFile
public java.lang.String getConfigFile()
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getOutput
public java.lang.String getOutput()
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headers
protected java.util.List<org.snpeff.vcf.VcfHeaderEntry> headers()
Headers to add
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init
public void init()
Initialize default values
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isOpt
protected boolean isOpt(java.lang.String arg)
Is this a command line option (e.g. "-tfam" is a command line option, but "-" means STDIN)
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loadConfig
protected void loadConfig()
Read config file
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openVcfInputFile
protected org.snpeff.fileIterator.VcfFileIterator openVcfInputFile()
Open VCF input file
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parseArgs
public void parseArgs(java.lang.String[] args)
Parse command line arguments- Specified by:
parseArgs
in interfaceorg.snpeff.snpEffect.commandLine.CommandLine
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processVcfHeader
protected java.lang.String processVcfHeader(org.snpeff.fileIterator.VcfFileIterator vcf)
Process VCF header related issues
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run
public boolean run()
- Specified by:
run
in interfaceorg.snpeff.snpEffect.commandLine.CommandLine
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setCommand
public void setCommand(java.lang.Class clss)
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setCommand
public void setCommand(java.lang.String command)
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setConfig
public void setConfig(org.snpeff.snpEffect.Config config)
- Specified by:
setConfig
in interfaceorg.snpeff.snpEffect.VcfAnnotator
-
setConfigFile
public void setConfigFile(java.lang.String configFile)
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setDbFileName
public void setDbFileName(java.lang.String dbFileName)
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setDebug
public void setDebug(boolean debug)
- Specified by:
setDebug
in interfaceorg.snpeff.snpEffect.VcfAnnotator
-
setQuiet
public void setQuiet(boolean quiet)
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setSaveOutput
public void setSaveOutput(boolean saveOutput)
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setShowVcfHeader
public void setShowVcfHeader(boolean showVcfHeader)
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setShowVersion
public void setShowVersion(boolean showVersion)
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setSuppressOutput
public void setSuppressOutput(boolean suppressOutput)
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setVcfHeaderAddProgramVersion
public void setVcfHeaderAddProgramVersion(boolean vcfHeaderAddProgramVersion)
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setVerbose
public void setVerbose(boolean verbose)
- Specified by:
setVerbose
in interfaceorg.snpeff.snpEffect.VcfAnnotator
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showCmd
public void showCmd()
Show command line
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showVersion
public void showVersion()
Show version number
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unSanitize
public java.lang.String unSanitize(java.lang.String str)
Convert a sanitized expression (from Galaxy) back to the original string References: http://www.mail-archive.com/galaxy-dev@lists.bx.psu.edu/msg00530.html
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usage
public void usage(java.lang.String msg)
Show usage message- Specified by:
usage
in interfaceorg.snpeff.snpEffect.commandLine.CommandLine
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usageGenericAndDb
protected void usageGenericAndDb()
Options common to all commands
-
-