Package picard.sam

Class CreateSequenceDictionary

  • @DocumentedFeature
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 Detail

      • OUTPUT

        @Argument(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

      • GENOME_ASSEMBLY

        @Argument(shortName="AS",
          doc="Put into AS field of sequence dictionary entry if supplied",
          optional=true)
public String GENOME_ASSEMBLY

      • URI

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

      • SPECIES

        @Argument(shortName="SP",
          doc="Put into SP field of sequence dictionary entry",
          optional=true)
public String SPECIES

      • TRUNCATE_NAMES_AT_WHITESPACE

        @Argument(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

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

      • ALT_NAMES

        @Argument(shortName="AN",
          doc="Optional file containing the alternative names for the contigs. Tools may use this information to consider different contig notations as identical (e.g: \'chr1\' and \'1\'). The alternative names will be put into the appropriate @AN annotation for each contig. No header. First column is the original name, the second column is an alternative name. One contig may have more than one alternative name.",
          optional=true)
public File ALT_NAMES

    • Constructor Detail

      • CreateSequenceDictionary

        public CreateSequenceDictionary()

    • Method Detail

      • makeSequenceDictionary

        public htsjdk.samtools.SAMSequenceDictionary makeSequenceDictionary​(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.

      • customCommandLineValidation

        protected 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.