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jannovar-cli, 0.20
A C D G H I J M P R S T 

A

AnnotateCSVCommand - Class in de.charite.compbio.jannovar.cmd.annotate_csv
Allows the annotation of a CVF file.
AnnotateCSVCommand(String[], Namespace) - Constructor for class de.charite.compbio.jannovar.cmd.annotate_csv.AnnotateCSVCommand
 
AnnotatedVCFWriter - Class in de.charite.compbio.jannovar.cmd.annotate_vcf
Annotate variant in VariantContext and write out through HTSJDK (i.e.
AnnotatedVCFWriter(ReferenceDictionary, VCFHeader, ImmutableMap<Integer, Chromosome>, String, JannovarAnnotateVCFOptions, ImmutableList<String>) - Constructor for class de.charite.compbio.jannovar.cmd.annotate_vcf.AnnotatedVCFWriter
 
AnnotatePositionCommand - Class in de.charite.compbio.jannovar.cmd.annotate_pos
Allows the annotation of a single position.
AnnotatePositionCommand(String[], Namespace) - Constructor for class de.charite.compbio.jannovar.cmd.annotate_pos.AnnotatePositionCommand
 
AnnotateVCFCommand - Class in de.charite.compbio.jannovar.cmd.annotate_vcf
Run annotation steps (read in VCF, write out VCF or Jannovar file format).
AnnotateVCFCommand(String[], Namespace) - Constructor for class de.charite.compbio.jannovar.cmd.annotate_vcf.AnnotateVCFCommand
 

C

close() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.AnnotatedVCFWriter
Close VariantContextWriter in out.
CommandLineParsingException - Exception in de.charite.compbio.jannovar.cmd
Exception thrown on problems with the command line.
CommandLineParsingException() - Constructor for exception de.charite.compbio.jannovar.cmd.CommandLineParsingException
 
CommandLineParsingException(String) - Constructor for exception de.charite.compbio.jannovar.cmd.CommandLineParsingException
 
CommandLineParsingException(String, Throwable) - Constructor for exception de.charite.compbio.jannovar.cmd.CommandLineParsingException
 

D

DatabaseListCommand - Class in de.charite.compbio.jannovar.cmd.db_list
 
DatabaseListCommand(String[], Namespace) - Constructor for class de.charite.compbio.jannovar.cmd.db_list.DatabaseListCommand
 
dataSourceFiles - Variable in class de.charite.compbio.jannovar.cmd.JannovarDBOptions
paths to INI files ot use for parsing
de.charite.compbio.jannovar - package de.charite.compbio.jannovar
 
de.charite.compbio.jannovar.cmd - package de.charite.compbio.jannovar.cmd
 
de.charite.compbio.jannovar.cmd.annotate_csv - package de.charite.compbio.jannovar.cmd.annotate_csv
 
de.charite.compbio.jannovar.cmd.annotate_pos - package de.charite.compbio.jannovar.cmd.annotate_pos
 
de.charite.compbio.jannovar.cmd.annotate_vcf - package de.charite.compbio.jannovar.cmd.annotate_vcf
 
de.charite.compbio.jannovar.cmd.db_list - package de.charite.compbio.jannovar.cmd.db_list
 
de.charite.compbio.jannovar.cmd.download - package de.charite.compbio.jannovar.cmd.download
 
de.charite.compbio.jannovar.cmd.hgvs_to_vcf - package de.charite.compbio.jannovar.cmd.hgvs_to_vcf
 
DownloadCommand - Class in de.charite.compbio.jannovar.cmd.download
Implementation of download step in Jannovar.
DownloadCommand(String[], Namespace) - Constructor for class de.charite.compbio.jannovar.cmd.download.DownloadCommand
 

G

getAlt() - Method in class de.charite.compbio.jannovar.cmd.annotate_csv.JannovarAnnotateCSVOptions
 
getChr() - Method in class de.charite.compbio.jannovar.cmd.annotate_csv.JannovarAnnotateCSVOptions
 
getCsv() - Method in class de.charite.compbio.jannovar.cmd.annotate_csv.JannovarAnnotateCSVOptions
 
getDatabaseFilePath() - Method in class de.charite.compbio.jannovar.cmd.JannovarAnnotationOptions
 
getDatabaseNames() - Method in class de.charite.compbio.jannovar.cmd.download.JannovarDownloadOptions
 
getDataSourceFiles() - Method in class de.charite.compbio.jannovar.cmd.JannovarDBOptions
 
getDownloadDir() - Method in class de.charite.compbio.jannovar.cmd.download.JannovarDownloadOptions
 
getFormat() - Method in class de.charite.compbio.jannovar.cmd.annotate_csv.JannovarAnnotateCSVOptions
 
getFtpProxy() - Method in class de.charite.compbio.jannovar.cmd.JannovarBaseOptions
 
getGenomicChanges() - Method in class de.charite.compbio.jannovar.cmd.annotate_pos.JannovarAnnotatePosOptions
 
getHttpProxy() - Method in class de.charite.compbio.jannovar.cmd.JannovarBaseOptions
 
getHttpsProxy() - Method in class de.charite.compbio.jannovar.cmd.JannovarBaseOptions
 
getPathInputText() - Method in class de.charite.compbio.jannovar.cmd.hgvs_to_vcf.ProjectTranscriptToChromosomeOptions
 
getPathInputVCF() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
getPathOutputVCF() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
getPathOutputVCF() - Method in class de.charite.compbio.jannovar.cmd.hgvs_to_vcf.ProjectTranscriptToChromosomeOptions
 
getPathReferenceFASTA() - Method in class de.charite.compbio.jannovar.cmd.hgvs_to_vcf.ProjectTranscriptToChromosomeOptions
 
getPos() - Method in class de.charite.compbio.jannovar.cmd.annotate_csv.JannovarAnnotateCSVOptions
 
getRef() - Method in class de.charite.compbio.jannovar.cmd.annotate_csv.JannovarAnnotateCSVOptions
 
getVCFHeader() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.AnnotatedVCFWriter
 
getVerbosity() - Method in class de.charite.compbio.jannovar.cmd.JannovarBaseOptions
 
getVersion() - Static method in class de.charite.compbio.jannovar.Jannovar
 

H

HelpRequestedException - Exception in de.charite.compbio.jannovar.cmd
Thrown when the user requests help.
HelpRequestedException() - Constructor for exception de.charite.compbio.jannovar.cmd.HelpRequestedException
 
HelpRequestedException(String) - Constructor for exception de.charite.compbio.jannovar.cmd.HelpRequestedException
 
HelpRequestedException(String, Throwable) - Constructor for exception de.charite.compbio.jannovar.cmd.HelpRequestedException
 

I

isEscapeAnnField() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
isHeader() - Method in class de.charite.compbio.jannovar.cmd.annotate_csv.JannovarAnnotateCSVOptions
 
isNt3PrimeShifting() - Method in class de.charite.compbio.jannovar.cmd.JannovarAnnotationOptions
 
isReportProgress() - Method in class de.charite.compbio.jannovar.cmd.JannovarBaseOptions
 
isShowAll() - Method in class de.charite.compbio.jannovar.cmd.JannovarAnnotationOptions
 
isUseThreeLetterAminoAcidCode() - Method in class de.charite.compbio.jannovar.cmd.JannovarAnnotationOptions
 

J

Jannovar - Class in de.charite.compbio.jannovar
This is the driver class for a program called Jannovar.
Jannovar() - Constructor for class de.charite.compbio.jannovar.Jannovar
 
JannovarAnnotateCSVOptions - Class in de.charite.compbio.jannovar.cmd.annotate_csv
Options for the annotate-pos comman
JannovarAnnotateCSVOptions() - Constructor for class de.charite.compbio.jannovar.cmd.annotate_csv.JannovarAnnotateCSVOptions
 
JannovarAnnotatePosOptions - Class in de.charite.compbio.jannovar.cmd.annotate_pos
Options for the annotate-pos comman
JannovarAnnotatePosOptions() - Constructor for class de.charite.compbio.jannovar.cmd.annotate_pos.JannovarAnnotatePosOptions
 
JannovarAnnotateVCFOptions - Class in de.charite.compbio.jannovar.cmd.annotate_vcf
Options for annotating VCF files
JannovarAnnotateVCFOptions() - Constructor for class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
JannovarAnnotationCommand - Class in de.charite.compbio.jannovar.cmd
Base class for commands needing annotation data.
JannovarAnnotationCommand() - Constructor for class de.charite.compbio.jannovar.cmd.JannovarAnnotationCommand
 
JannovarAnnotationOptions - Class in de.charite.compbio.jannovar.cmd
Configuration for the annotation commands
JannovarAnnotationOptions() - Constructor for class de.charite.compbio.jannovar.cmd.JannovarAnnotationOptions
 
JannovarBaseOptions - Class in de.charite.compbio.jannovar.cmd
Base option class for global Jannovar options
JannovarBaseOptions() - Constructor for class de.charite.compbio.jannovar.cmd.JannovarBaseOptions
 
JannovarCommand - Class in de.charite.compbio.jannovar.cmd
Super class for all commands, i.e.
JannovarCommand() - Constructor for class de.charite.compbio.jannovar.cmd.JannovarCommand
 
JannovarDBListOptions - Class in de.charite.compbio.jannovar.cmd.db_list
Configuration for the db-list command
JannovarDBListOptions() - Constructor for class de.charite.compbio.jannovar.cmd.db_list.JannovarDBListOptions
 
JannovarDBOptions - Class in de.charite.compbio.jannovar.cmd
Configuration for database-related commands in Jannovar
JannovarDBOptions() - Constructor for class de.charite.compbio.jannovar.cmd.JannovarDBOptions
 
JannovarDownloadOptions - Class in de.charite.compbio.jannovar.cmd.download
Configuration for the download command
JannovarDownloadOptions() - Constructor for class de.charite.compbio.jannovar.cmd.download.JannovarDownloadOptions
 

M

main(String[]) - Static method in class de.charite.compbio.jannovar.Jannovar
 

P

pathFASTARef - Variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
Path to the reference FAI-indexed FASTA file (required for dbSNP/ExAC/UK10K-based annotation
pathPedFile - Variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
Path to pedigree file
pathVCFDBSNP - Variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
Path to dbSNP VCF file to use for the annotation
pathVCFExac - Variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
Path to ExAC VCF file to use for the annotation
pathVCFUK10K - Variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
Path to UK10K VCF file to use for the annotation
prefixDBSNP - Variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
Prefix to use for dbSNP VCF INFO Fields
prefixExac - Variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
Prefix to use for ExAC VCF INFO Fields
prefixUK10K - Variable in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
Prefix to use for UK10K VCF INFO Fields
ProjectTranscriptToChromosome - Class in de.charite.compbio.jannovar.cmd.hgvs_to_vcf
Project transcript to chromosomal changes
ProjectTranscriptToChromosome(String[], Namespace) - Constructor for class de.charite.compbio.jannovar.cmd.hgvs_to_vcf.ProjectTranscriptToChromosome
 
ProjectTranscriptToChromosomeOptions - Class in de.charite.compbio.jannovar.cmd.hgvs_to_vcf
Projection from transcript-level to chromosome-level changes
ProjectTranscriptToChromosomeOptions() - Constructor for class de.charite.compbio.jannovar.cmd.hgvs_to_vcf.ProjectTranscriptToChromosomeOptions
 
put(VariantContext) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.AnnotatedVCFWriter
 

R

run() - Method in class de.charite.compbio.jannovar.cmd.annotate_csv.AnnotateCSVCommand
This function will simply annotate a csv file wehere positions are set
run() - Method in class de.charite.compbio.jannovar.cmd.annotate_pos.AnnotatePositionCommand
This function will simply annotate given chromosomal position with HGVS compliant output.
run() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.AnnotateVCFCommand
This function inputs a VCF file, and prints the annotated version thereof to a file (name of the original file with the suffix .de.charite.compbio.jannovar).
run() - Method in class de.charite.compbio.jannovar.cmd.db_list.DatabaseListCommand
Perform the downloading.
run() - Method in class de.charite.compbio.jannovar.cmd.download.DownloadCommand
Perform the downloading.
run() - Method in class de.charite.compbio.jannovar.cmd.hgvs_to_vcf.ProjectTranscriptToChromosome
 
run() - Method in class de.charite.compbio.jannovar.cmd.JannovarCommand
Function for the execution of the command.

S

setDatabaseFilePath(String) - Method in class de.charite.compbio.jannovar.cmd.JannovarAnnotationOptions
 
setDatabaseNames(List<String>) - Method in class de.charite.compbio.jannovar.cmd.download.JannovarDownloadOptions
 
setDataSourceFiles(List<String>) - Method in class de.charite.compbio.jannovar.cmd.JannovarDBOptions
 
setDownloadDir(String) - Method in class de.charite.compbio.jannovar.cmd.download.JannovarDownloadOptions
 
setEscapeAnnField(boolean) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setFromArgs(Namespace) - Method in class de.charite.compbio.jannovar.cmd.annotate_csv.JannovarAnnotateCSVOptions
 
setFromArgs(Namespace) - Method in class de.charite.compbio.jannovar.cmd.annotate_pos.JannovarAnnotatePosOptions
 
setFromArgs(Namespace) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setFromArgs(Namespace) - Method in class de.charite.compbio.jannovar.cmd.download.JannovarDownloadOptions
 
setFromArgs(Namespace) - Method in class de.charite.compbio.jannovar.cmd.hgvs_to_vcf.ProjectTranscriptToChromosomeOptions
 
setFromArgs(Namespace) - Method in class de.charite.compbio.jannovar.cmd.JannovarAnnotationOptions
 
setFromArgs(Namespace) - Method in class de.charite.compbio.jannovar.cmd.JannovarBaseOptions
Get values from Namespace object
setFromArgs(Namespace) - Method in class de.charite.compbio.jannovar.cmd.JannovarDBOptions
 
setFtpProxy(URL) - Method in class de.charite.compbio.jannovar.cmd.JannovarBaseOptions
 
setGenomicChanges(List<String>) - Method in class de.charite.compbio.jannovar.cmd.annotate_pos.JannovarAnnotatePosOptions
 
setHttpProxy(URL) - Method in class de.charite.compbio.jannovar.cmd.JannovarBaseOptions
 
setHttpsProxy(URL) - Method in class de.charite.compbio.jannovar.cmd.JannovarBaseOptions
 
setNt3PrimeShifting(boolean) - Method in class de.charite.compbio.jannovar.cmd.JannovarAnnotationOptions
 
setPathInputText(String) - Method in class de.charite.compbio.jannovar.cmd.hgvs_to_vcf.ProjectTranscriptToChromosomeOptions
 
setPathInputVCF(String) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setPathOutputVCF(String) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
setPathOutputVCF(String) - Method in class de.charite.compbio.jannovar.cmd.hgvs_to_vcf.ProjectTranscriptToChromosomeOptions
 
setPathReferenceFASTA(String) - Method in class de.charite.compbio.jannovar.cmd.hgvs_to_vcf.ProjectTranscriptToChromosomeOptions
 
setReportProgress(boolean) - Method in class de.charite.compbio.jannovar.cmd.JannovarBaseOptions
 
setShowAll(boolean) - Method in class de.charite.compbio.jannovar.cmd.JannovarAnnotationOptions
 
setupParser(Subparsers) - Static method in class de.charite.compbio.jannovar.cmd.annotate_csv.JannovarAnnotateCSVOptions
Setup ArgumentParser
setupParser(Subparsers) - Static method in class de.charite.compbio.jannovar.cmd.annotate_pos.JannovarAnnotatePosOptions
Setup ArgumentParser
setupParser(Subparsers) - Static method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
Setup ArgumentParser
setupParser(Subparsers) - Static method in class de.charite.compbio.jannovar.cmd.db_list.JannovarDBListOptions
Setup ArgumentParser
setupParser(Subparsers) - Static method in class de.charite.compbio.jannovar.cmd.download.JannovarDownloadOptions
Setup ArgumentParser
setupParser(Subparsers) - Static method in class de.charite.compbio.jannovar.cmd.hgvs_to_vcf.ProjectTranscriptToChromosomeOptions
Setup ArgumentParser
setupParser(ArgumentParser) - Static method in class de.charite.compbio.jannovar.cmd.JannovarAnnotationOptions
Setup ArgumentParser
setupParser(ArgumentParser) - Static method in class de.charite.compbio.jannovar.cmd.JannovarBaseOptions
Setup global ArgumentParser
setUseThreeLetterAminoAcidCode(boolean) - Method in class de.charite.compbio.jannovar.cmd.JannovarAnnotationOptions
 
setVerbosity(int) - Method in class de.charite.compbio.jannovar.cmd.JannovarBaseOptions
 

T

toString() - Method in class de.charite.compbio.jannovar.cmd.annotate_csv.JannovarAnnotateCSVOptions
 
toString() - Method in class de.charite.compbio.jannovar.cmd.annotate_pos.JannovarAnnotatePosOptions
 
toString() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.JannovarAnnotateVCFOptions
 
toString() - Method in class de.charite.compbio.jannovar.cmd.download.JannovarDownloadOptions
 
toString() - Method in class de.charite.compbio.jannovar.cmd.hgvs_to_vcf.ProjectTranscriptToChromosomeOptions
 
toString() - Method in class de.charite.compbio.jannovar.cmd.JannovarAnnotationOptions
 
toString() - Method in class de.charite.compbio.jannovar.cmd.JannovarBaseOptions
 
toString() - Method in class de.charite.compbio.jannovar.cmd.JannovarDBOptions
 
A C D G H I J M P R S T 
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jannovar-cli, 0.20

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