picard.sam

Class CreateSequenceDictionary

java.lang.Object

picard.cmdline.CommandLineProgram

picard.sam.CreateSequenceDictionary

public class CreateSequenceDictionary
extends CommandLineProgram

Create a SAM/BAM file from a fasta containing reference sequence. The output SAM file contains a header but no SAMRecords, and the header contains only sequence records.

Field Summary

Fields

Modifier and Type	Field and Description
java.lang.String	GENOME_ASSEMBLY
int	NUM_SEQUENCES
java.io.File	OUTPUT
java.io.File	REFERENCE
java.lang.String	SPECIES
boolean	TRUNCATE_NAMES_AT_WHITESPACE
java.lang.String	URI

Fields inherited from class picard.cmdline.CommandLineProgram

COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, TMP_DIR, VALIDATION_STRINGENCY, VERBOSITY

Constructor Summary

Constructors

Constructor and Description
CreateSequenceDictionary()

Method Summary

Modifier and Type	Method and Description
protected java.lang.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(java.lang.String[] argv)
htsjdk.samtools.SAMSequenceDictionary	makeSequenceDictionary(java.io.File referenceFile) Read all the sequences from the given reference file, and convert into SAMSequenceRecords

Methods inherited from class picard.cmdline.CommandLineProgram

getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

REFERENCE

@Option(doc="Input reference fasta or fasta.gz",
        shortName="R")
public java.io.File REFERENCE

OUTPUT

@Option(doc="Output SAM or BAM file containing only the sequence dictionary",
        shortName="O")
public java.io.File OUTPUT

GENOME_ASSEMBLY

@Option(doc="Put into AS field of sequence dictionary entry if supplied",
        optional=true)
public java.lang.String GENOME_ASSEMBLY

URI

@Option(doc="Put into UR field of sequence dictionary entry.  If not supplied, input reference file is used",
        optional=true)
public java.lang.String URI

SPECIES

@Option(doc="Put into SP field of sequence dictionary entry",
        optional=true)
public java.lang.String SPECIES

TRUNCATE_NAMES_AT_WHITESPACE

@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

NUM_SEQUENCES

@Option(doc="Stop after writing this many sequences.  For testing.")
public int NUM_SEQUENCES

Constructor Detail

CreateSequenceDictionary

public CreateSequenceDictionary()

Method Detail

main

public static void main(java.lang.String[] argv)

customCommandLineValidation

protected java.lang.String[] customCommandLineValidation()

Use reference filename to create URI to go into header if URI was not passed on cmd line.

Overrides:

customCommandLineValidation in class CommandLineProgram

Returns:

null if command line is valid. If command line is invalid, returns an array of error message to be written to the appropriate place.

doWork

protected int doWork()

Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.

Specified by:

doWork in class CommandLineProgram

Returns:

program exit status.

makeSequenceDictionary

public htsjdk.samtools.SAMSequenceDictionary makeSequenceDictionary(java.io.File referenceFile)

Read all the sequences from the given reference file, and convert into SAMSequenceRecords

Parameters:

referenceFile - fasta or fasta.gz

Returns:

SAMSequenceRecords containing info from the fasta, plus from cmd-line arguments.