Package picard.annotation
Class SortGff
- java.lang.Object
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- picard.cmdline.CommandLineProgram
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- picard.annotation.SortGff
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public class SortGff extends CommandLineProgram
Summary
This tool sorts a gff3 file by coordinates, so that it can be indexed. It additionally adds flush directives where possible, which can significantly reduce the memory footprint of downstream tools. Sorting of multiple contigs can be specified by a sequence dictionary; if no sequence dictionary is specified, contigs are sorted lexicographically.
Usage Examples
1. Sort gff3 file, add flush directives. Contigs will be sorted lexicographically.
java -jar picard.jar SortGff I=input.gff3 O=output.gff3
2. Sort gff3 file, add flush directives. Contigs will be sorted according to order in sequence dictionary
java -jar picard.jar SortGff I=input.gff3 O=output.gff3 SD=dictionary.dict
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Field Summary
Fields Modifier and Type Field Description File
INPUT
int
nRecordsInMemory
File
OUTPUT
File
SEQUENCE_DICTIONARY
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Fields inherited from class picard.cmdline.CommandLineProgram
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, SYNTAX_TRANSITION_URL, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY
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Constructor Summary
Constructors Constructor Description SortGff()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected int
doWork()
Do the work after command line has been parsed.-
Methods inherited from class picard.cmdline.CommandLineProgram
checkRInstallation, customCommandLineValidation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
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Field Detail
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INPUT
@Argument(doc="Input Gff3 file to sort.", shortName="I") public File INPUT
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OUTPUT
@Argument(doc="Sorted Gff3 output file.", shortName="O") public File OUTPUT
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SEQUENCE_DICTIONARY
@Argument(doc="Dictionary to sort contigs by. If dictionary is not provided, contigs are sorted lexicographically.", shortName="SD", optional=true) public File SEQUENCE_DICTIONARY
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nRecordsInMemory
@Argument(doc="Number of records to hold in memory before spilling to disk", optional=true) public int nRecordsInMemory
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Method Detail
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doWork
protected int doWork()
Description copied from class:CommandLineProgram
Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.- Specified by:
doWork
in classCommandLineProgram
- Returns:
- program exit status.
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