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A

AnnotatedJannovarWriter - Class in de.charite.compbio.jannovar.cmd.annotate_vcf
Annotate variant in VariantContext and write out in Jannovar format.
AnnotatedJannovarWriter(ReferenceDictionary, ImmutableMap<Integer, Chromosome>, String, JannovarOptions) - Constructor for class de.charite.compbio.jannovar.cmd.annotate_vcf.AnnotatedJannovarWriter
 
AnnotatedVariantWriter - Class in de.charite.compbio.jannovar.cmd.annotate_vcf
Interface for output writers in Jannovar class.
AnnotatedVariantWriter() - Constructor for class de.charite.compbio.jannovar.cmd.annotate_vcf.AnnotatedVariantWriter
 
AnnotatedVCFWriter - Class in de.charite.compbio.jannovar.cmd.annotate_vcf
Annotate variant in VariantContext and write out through HTSJDK (i.e.
AnnotatedVCFWriter(ReferenceDictionary, VCFFileReader, ImmutableMap<Integer, Chromosome>, String, JannovarOptions, 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[]) - Constructor for class de.charite.compbio.jannovar.cmd.annotate_pos.AnnotatePositionCommand
 
AnnotatePositionCommandLineParser - Class in de.charite.compbio.jannovar.cmd.annotate_pos
Parse the command line for the "annotate-position" command.
AnnotatePositionCommandLineParser() - Constructor for class de.charite.compbio.jannovar.cmd.annotate_pos.AnnotatePositionCommandLineParser
 
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[]) - Constructor for class de.charite.compbio.jannovar.cmd.annotate_vcf.AnnotateVCFCommand
 
AnnotateVCFCommandLineParser - Class in de.charite.compbio.jannovar.cmd.annotate_vcf
Parser for annotate-vcf command line.
AnnotateVCFCommandLineParser() - Constructor for class de.charite.compbio.jannovar.cmd.annotate_vcf.AnnotateVCFCommandLineParser
 
args - Variable in class de.charite.compbio.jannovar.cmd.JannovarCommand
command line arguments

C

chromosomalChanges - Variable in class de.charite.compbio.jannovar.JannovarOptions
chromosomal position and a change, e.g.
chromosomeMap - Variable in class de.charite.compbio.jannovar.cmd.JannovarAnnotationCommand
Map of Chromosomes, used in the annotation.
close() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.AnnotatedJannovarWriter
Close writer, free resources
close() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.AnnotatedVCFWriter
Close VariantContextWriter in out.
command - Variable in class de.charite.compbio.jannovar.JannovarOptions
the selected command
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[]) - Constructor for class de.charite.compbio.jannovar.cmd.db_list.DatabaseListCommand
 
DatabaseListCommandLineParser - Class in de.charite.compbio.jannovar.cmd.db_list
 
DatabaseListCommandLineParser() - Constructor for class de.charite.compbio.jannovar.cmd.db_list.DatabaseListCommandLineParser
Calls initializeParser().
dataFile - Variable in class de.charite.compbio.jannovar.JannovarOptions
path to the file with the serialized data
dataSourceFiles - Variable in class de.charite.compbio.jannovar.JannovarOptions
paths to INI files ot use for parsing
dataSourceNames - Variable in class de.charite.compbio.jannovar.JannovarOptions
data source name to use for downloading and 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_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
 
deserializeTranscriptDefinitionFile() - Method in class de.charite.compbio.jannovar.cmd.JannovarAnnotationCommand
Deserialize the transcript definition file, as configured in JannovarCommand.options.
DownloadCommand - Class in de.charite.compbio.jannovar.cmd.download
Implementation of download step in Jannovar.
DownloadCommand(String[]) - Constructor for class de.charite.compbio.jannovar.cmd.download.DownloadCommand
 
DownloadCommandLineParser - Class in de.charite.compbio.jannovar.cmd.download
Helper class for parsing the commandline of the download command.
DownloadCommandLineParser() - Constructor for class de.charite.compbio.jannovar.cmd.download.DownloadCommandLineParser
Calls initializeParser().
downloadPath - Variable in class de.charite.compbio.jannovar.JannovarOptions
directory to use for the downloads and the serialized file

E

escapeAnnField - Variable in class de.charite.compbio.jannovar.JannovarOptions
whether or not to escape characters like '=' in the ANN VCF field.

F

ftpProxy - Variable in class de.charite.compbio.jannovar.JannovarOptions
proxy for FTP

G

getOutFileName() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.AnnotatedJannovarWriter
 
getOutFileName() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.AnnotatedVariantWriter
Returns output path
getOutFileName() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.AnnotatedVCFWriter
Create and return output file name.

H

helpOptions - Variable in class de.charite.compbio.jannovar.cmd.download.DownloadCommandLineParser
 
helpOptions - Variable in class de.charite.compbio.jannovar.cmd.JannovarAnnotationCommandLineParser
option to catch the help option if set
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
 
httpProxy - Variable in class de.charite.compbio.jannovar.JannovarOptions
proxy for HTTP
httpsProxy - Variable in class de.charite.compbio.jannovar.JannovarOptions
proxy for HTTPS

I

initializeParser() - Method in class de.charite.compbio.jannovar.cmd.annotate_pos.AnnotatePositionCommandLineParser
 
initializeParser() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.AnnotateVCFCommandLineParser
 
initializeParser() - Method in class de.charite.compbio.jannovar.cmd.JannovarAnnotationCommandLineParser

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
 
JANNOVAR_VERSION - Static variable in class de.charite.compbio.jannovar.JannovarOptions
the version of the program
JannovarAnnotationCommand - Class in de.charite.compbio.jannovar.cmd
Base class for commands needing annotation data.
JannovarAnnotationCommand(String[]) - Constructor for class de.charite.compbio.jannovar.cmd.JannovarAnnotationCommand
 
JannovarAnnotationCommandLineParser - Class in de.charite.compbio.jannovar.cmd
Base class for the command line parser for the annotation commands.
JannovarAnnotationCommandLineParser() - Constructor for class de.charite.compbio.jannovar.cmd.JannovarAnnotationCommandLineParser
Calls initializeParser().
JannovarCommand - Class in de.charite.compbio.jannovar.cmd
Super class for all commands, i.e.
JannovarCommand(String[]) - Constructor for class de.charite.compbio.jannovar.cmd.JannovarCommand
Initialize the JannovarCommand.
jannovarFormat - Variable in class de.charite.compbio.jannovar.JannovarOptions
whether to write the result in the Jannovar format
JannovarOptions - Class in de.charite.compbio.jannovar
Configuration for the Jannovar program.
JannovarOptions() - Constructor for class de.charite.compbio.jannovar.JannovarOptions
 
JannovarOptions.Command - Enum in de.charite.compbio.jannovar
The command that is to be executed.

M

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

N

nt3PrimeShifting - Variable in class de.charite.compbio.jannovar.JannovarOptions
whether or not to shift variants towards the 3' end of the transcript

O

options - Variable in class de.charite.compbio.jannovar.cmd.db_list.DatabaseListCommandLineParser
options representation for the Apache commons command line parser
options - Variable in class de.charite.compbio.jannovar.cmd.download.DownloadCommandLineParser
options representation for the Apache commons command line parser
options - Variable in class de.charite.compbio.jannovar.cmd.JannovarAnnotationCommandLineParser
options representation for the Apache commons command line parser
options - Variable in class de.charite.compbio.jannovar.cmd.JannovarCommand
Configuration to use for the command execution.
outputInfix - Variable in class de.charite.compbio.jannovar.JannovarOptions
infix added to output file name before .vcf/.vcf.gz/.bcf output
outVCFFile - Variable in class de.charite.compbio.jannovar.JannovarOptions
path to output VCF file path (overrides generation of file name from input file name)
outVCFFolder - Variable in class de.charite.compbio.jannovar.JannovarOptions
path to output folder for the annotated VCF files (default is parallel to input file)

P

parse(String[]) - Method in class de.charite.compbio.jannovar.cmd.annotate_pos.AnnotatePositionCommandLineParser
 
parse(String[]) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.AnnotateVCFCommandLineParser
 
parse(String[]) - Method in class de.charite.compbio.jannovar.cmd.db_list.DatabaseListCommandLineParser
Parse the command line and
parse(String[]) - Method in class de.charite.compbio.jannovar.cmd.download.DownloadCommandLineParser
Parse the command line and
parse(String[]) - Method in class de.charite.compbio.jannovar.cmd.JannovarAnnotationCommandLineParser
Parse command line arguments and return JannovarOptions.
parseCommandLine(String[]) - Method in class de.charite.compbio.jannovar.cmd.annotate_pos.AnnotatePositionCommand
 
parseCommandLine(String[]) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.AnnotateVCFCommand
 
parseCommandLine(String[]) - Method in class de.charite.compbio.jannovar.cmd.db_list.DatabaseListCommand
 
parseCommandLine(String[]) - Method in class de.charite.compbio.jannovar.cmd.download.DownloadCommand
 
parseCommandLine(String[]) - Method in class de.charite.compbio.jannovar.cmd.JannovarCommand
Function for parsing the command line.
parser - Variable in class de.charite.compbio.jannovar.cmd.db_list.DatabaseListCommandLineParser
the Apache commons command line parser
parser - Variable in class de.charite.compbio.jannovar.cmd.download.DownloadCommandLineParser
the Apache commons command line parser
parser - Variable in class de.charite.compbio.jannovar.cmd.JannovarAnnotationCommandLineParser
the Apache commons command line parser
print(PrintStream) - Method in class de.charite.compbio.jannovar.JannovarOptions
Print option values to stderr.
printHelp() - Method in class de.charite.compbio.jannovar.cmd.annotate_pos.AnnotatePositionCommandLineParser
 
printHelp() - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.AnnotateVCFCommandLineParser
 
printHelp() - Method in class de.charite.compbio.jannovar.cmd.JannovarAnnotationCommandLineParser
 
printHelpIfOptionIsSet(CommandLine) - Method in class de.charite.compbio.jannovar.cmd.JannovarAnnotationCommandLineParser
 
printProgressBars - Variable in class de.charite.compbio.jannovar.JannovarOptions
whether to print progress bars to stderr or not.
put(VariantContext) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.AnnotatedJannovarWriter
Write out record for VariantContext.
put(VariantContext) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.AnnotatedVariantWriter
Write out the given VariantContext with additional annotation.
put(VariantContext) - Method in class de.charite.compbio.jannovar.cmd.annotate_vcf.AnnotatedVCFWriter
 

R

refDict - Variable in class de.charite.compbio.jannovar.cmd.JannovarAnnotationCommand
ReferenceDictionary with genome information.
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.JannovarCommand
Function for the execution of the command.

S

showAll - Variable in class de.charite.compbio.jannovar.JannovarOptions
whether to report the annotations for all affected transcripts for each alternative allele

V

valueOf(String) - Static method in enum de.charite.compbio.jannovar.JannovarOptions.Command
Returns the enum constant of this type with the specified name.
values() - Static method in enum de.charite.compbio.jannovar.JannovarOptions.Command
Returns an array containing the constants of this enum type, in the order they are declared.
vcfFilePaths - Variable in class de.charite.compbio.jannovar.JannovarOptions
path to a VCF file to be annotated
verbosity - Variable in class de.charite.compbio.jannovar.cmd.JannovarCommand
Verbosity level: (0) quiet, (1) normal, (2) verbose, (3) very verbose
verbosity - Variable in class de.charite.compbio.jannovar.JannovarOptions
verbosity level

W

writeJannovarInfoFields - Variable in class de.charite.compbio.jannovar.JannovarOptions
whether or not to write out the old Jannovar annotation VCF tags
writeVCFAnnotationStandardInfoFields - Variable in class de.charite.compbio.jannovar.JannovarOptions
whether or not to write out the VCF annotation standard fields
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