public class JannovarAnnotateVCFOptions extends JannovarAnnotationOptions
| Modifier and Type | Field and Description |
|---|---|
String |
pathFASTARef
Path to the reference FAI-indexed FASTA file (required for dbSNP/ExAC/UK10K-based annotation
|
String |
pathPedFile
Path to pedigree file
|
String |
pathVCFDBSNP
Path to dbSNP VCF file to use for the annotation
|
String |
pathVCFExac
Path to ExAC VCF file to use for the annotation
|
String |
pathVCFUK10K
Path to UK10K VCF file to use for the annotation
|
String |
prefixDBSNP
Prefix to use for dbSNP VCF INFO Fields
|
String |
prefixExac
Prefix to use for ExAC VCF INFO Fields
|
String |
prefixUK10K
Prefix to use for UK10K VCF INFO Fields
|
| Constructor and Description |
|---|
JannovarAnnotateVCFOptions() |
| Modifier and Type | Method and Description |
|---|---|
String |
getPathInputVCF() |
String |
getPathOutputVCF() |
boolean |
isEscapeAnnField() |
void |
setEscapeAnnField(boolean escapeAnnField) |
void |
setFromArgs(net.sourceforge.argparse4j.inf.Namespace args)
Get values from
Namespace object |
void |
setPathInputVCF(String pathInputVCF) |
void |
setPathOutputVCF(String pathOutputVCF) |
static void |
setupParser(net.sourceforge.argparse4j.inf.Subparsers subParsers)
Setup
ArgumentParser |
String |
toString() |
getDatabaseFilePath, isNt3PrimeShifting, isShowAll, isUseThreeLetterAminoAcidCode, setDatabaseFilePath, setNt3PrimeShifting, setShowAll, setupParser, setUseThreeLetterAminoAcidCodegetFtpProxy, getHttpProxy, getHttpsProxy, getVerbosity, isReportProgress, setFtpProxy, setHttpProxy, setHttpsProxy, setReportProgress, setVerbositypublic String pathVCFDBSNP
public String prefixDBSNP
public String pathFASTARef
public String pathVCFExac
public String prefixExac
public String pathVCFUK10K
public String prefixUK10K
public String pathPedFile
public static void setupParser(net.sourceforge.argparse4j.inf.Subparsers subParsers)
ArgumentParsersubParsers - Subparsers to setuppublic void setFromArgs(net.sourceforge.argparse4j.inf.Namespace args)
throws CommandLineParsingException
JannovarBaseOptionsNamespace objectsetFromArgs in class JannovarAnnotationOptionsargs - Namespace to get the option values fromCommandLineParsingException - on problems parsing a given URLpublic String getPathInputVCF()
public void setPathInputVCF(String pathInputVCF)
public String getPathOutputVCF()
public void setPathOutputVCF(String pathOutputVCF)
public boolean isEscapeAnnField()
public void setEscapeAnnField(boolean escapeAnnField)
public String toString()
toString in class JannovarAnnotationOptionsCopyright © 2016. All rights reserved.