public final class JannovarOptions extends Object
Modifier and Type | Class and Description |
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static class |
JannovarOptions.Command
The command that is to be executed.
|
Modifier and Type | Field and Description |
---|---|
ArrayList<String> |
chromosomalChanges
chromosomal position and a change, e.g.
|
JannovarOptions.Command |
command
the selected command
|
String |
dataFile
path to the file with the serialized data
|
com.google.common.collect.ImmutableList<String> |
dataSourceFiles
paths to INI files ot use for parsing
|
com.google.common.collect.ImmutableList<String> |
dataSourceNames
data source name to use for downloading and parsing
|
String |
downloadPath
directory to use for the downloads and the serialized file
|
boolean |
escapeAnnField
whether or not to escape characters like
'=' in the ANN VCF field. |
URL |
ftpProxy
proxy for FTP
|
URL |
httpProxy
proxy for HTTP
|
URL |
httpsProxy
proxy for HTTPS
|
static String |
JANNOVAR_VERSION
the version of the program
|
boolean |
nt3PrimeShifting
whether or not to shift variants towards the 3' end of the transcript
|
String |
outputInfix
infix added to output file name before .vcf/.vcf.gz/.bcf output
|
String |
outVCFFile
path to output VCF file path (overrides generation of file name from input file name)
|
String |
outVCFFolder
path to output folder for the annotated VCF files (default is parallel to input file)
|
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
|
boolean |
printProgressBars
whether to print progress bars to stderr or not.
|
boolean |
showAll
whether to report the annotations for all affected transcripts for each alternative allele
|
boolean |
useThreeLetterAminoAcidCode
whether to use 3 letter amino acid code instead of 1 letter
|
ArrayList<String> |
vcfFilePaths
path to a VCF file to be annotated
|
int |
verbosity
verbosity level
|
boolean |
writeJannovarInfoFields
whether or not to write out the old Jannovar annotation VCF tags
|
boolean |
writeVCFAnnotationStandardInfoFields
whether or not to write out the VCF annotation standard fields
|
Constructor and Description |
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JannovarOptions() |
Modifier and Type | Method and Description |
---|---|
void |
print(PrintStream out)
Print option values to stderr.
|
public static final String JANNOVAR_VERSION
public JannovarOptions.Command command
public boolean printProgressBars
public int verbosity
public com.google.common.collect.ImmutableList<String> dataSourceFiles
public com.google.common.collect.ImmutableList<String> dataSourceNames
public String downloadPath
public URL httpProxy
public URL httpsProxy
public URL ftpProxy
public String dataFile
public boolean showAll
public String outVCFFolder
public boolean writeJannovarInfoFields
public boolean writeVCFAnnotationStandardInfoFields
public boolean useThreeLetterAminoAcidCode
public boolean escapeAnnField
'='
in the ANN
VCF field.public boolean nt3PrimeShifting
public String outputInfix
public String outVCFFile
public String pathVCFDBSNP
public String prefixDBSNP
public String pathFASTARef
public String pathVCFExac
public String prefixExac
public String pathVCFUK10K
public String prefixUK10K
public String pathPedFile
public void print(PrintStream out)
out
- Stream to print to.Copyright © 2016. All rights reserved.