public final class JannovarOptions extends Object
Modifier and Type | Class and Description |
---|---|
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 |
jannovarFormat
whether to write the result in the Jannovar format
|
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)
|
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
|
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 |
---|
JannovarOptions() |
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 jannovarFormat
public boolean showAll
public String outVCFFolder
public boolean writeJannovarInfoFields
public boolean writeVCFAnnotationStandardInfoFields
public boolean escapeAnnField
'='
in the ANN
VCF field.public boolean nt3PrimeShifting
public String outputInfix
public String outVCFFile
public void print(PrintStream out)
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