public class CreateSequenceDictionary extends CommandLineProgram
Modifier and Type | Field | Description |
---|---|---|
String |
GENOME_ASSEMBLY |
|
int |
NUM_SEQUENCES |
|
File |
OUTPUT |
|
File |
REFERENCE |
|
String |
SPECIES |
|
boolean |
TRUNCATE_NAMES_AT_WHITESPACE |
|
String |
URI |
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, TMP_DIR, VALIDATION_STRINGENCY, VERBOSITY
Constructor | Description |
---|---|
CreateSequenceDictionary() |
Modifier and Type | Method | Description |
---|---|---|
protected String[] |
customCommandLineValidation() |
Use reference filename to create URI to go into header if URI was not passed on cmd line.
|
protected int |
doWork() |
Do the work after command line has been parsed.
|
static void |
main(String[] argv) |
|
htsjdk.samtools.SAMSequenceDictionary |
makeSequenceDictionary(File referenceFile) |
Deprecated.
|
getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders
@Option(doc="Output SAM file containing only the sequence dictionary. By default it will use the base name of the input reference with the .dict extension", shortName="O", optional=true) public File OUTPUT
@Option(doc="Put into AS field of sequence dictionary entry if supplied", optional=true) public String GENOME_ASSEMBLY
@Option(doc="Put into UR field of sequence dictionary entry. If not supplied, input reference file is used", optional=true) public String URI
@Option(doc="Put into SP field of sequence dictionary entry", optional=true) public String SPECIES
@Option(doc="Make sequence name the first word from the > line in the fasta file. By default the entire contents of the > line is used, excluding leading and trailing whitespace.") public boolean TRUNCATE_NAMES_AT_WHITESPACE
public static void main(String[] argv)
@Deprecated public htsjdk.samtools.SAMSequenceDictionary makeSequenceDictionary(File referenceFile)
referenceFile
- fasta or fasta.gzprotected String[] customCommandLineValidation()
customCommandLineValidation
in class CommandLineProgram
protected int doWork()
doWork
in class CommandLineProgram