public abstract class JannovarAnnotationCommand extends JannovarCommand
Modifier and Type | Field and Description |
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protected com.google.common.collect.ImmutableMap<Integer,Chromosome> |
chromosomeMap
Map of Chromosomes, used in the annotation.
|
protected ReferenceDictionary |
refDict
ReferenceDictionary with genome information. |
args, options, verbosity
Constructor and Description |
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JannovarAnnotationCommand(String[] argv) |
Modifier and Type | Method and Description |
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protected void |
deserializeTranscriptDefinitionFile()
Deserialize the transcript definition file, as configured in
JannovarCommand.options . |
parseCommandLine, run
protected ReferenceDictionary refDict
ReferenceDictionary
with genome information.protected com.google.common.collect.ImmutableMap<Integer,Chromosome> chromosomeMap
public JannovarAnnotationCommand(String[] argv) throws CommandLineParsingException, HelpRequestedException
protected void deserializeTranscriptDefinitionFile() throws JannovarException, HelpRequestedException
JannovarCommand.options
.
To run Jannovar, the user must pass a transcript definition file with the -D flag. This can be one of the files
ucsc.ser, ensembl.ser, or refseq.ser (or a comparable file) containing a serialized version of the
TranscriptModel objects created to contain info about the transcript definitions (exon positions etc.) extracted
from UCSC, Ensembl, or Refseq and necessary for annotation.JannovarException
- when there is a problem with the deserializationHelpRequestedException
- when the user requested the help pageCopyright © 2016. All rights reserved.