Field Detail

• INPUT

  @Argument(doc="The SAM or BAM file that will be filtered.",
            shortName="I")
  public File INPUT

• FILTER

  @Argument(doc="Which filter to use.")
  public FilterSamReads.Filter FILTER

• READ_LIST_FILE

  @Argument(doc="File containing reads that will be included in or excluded from the OUTPUT SAM or BAM file, when using FILTER=includeReadList or FILTER=includeReadList.",
            optional=true,
            shortName="RLF")
  public File READ_LIST_FILE

• INTERVAL_LIST

  @Argument(doc="Interval List File containing intervals that will be included in the OUTPUT when using FILTER=includePairedIntervals",
            optional=true,
            shortName="IL")
  public File INTERVAL_LIST

• TAG

  @Argument(doc="The tag to select from input SAM/BAM",
            optional=true,
            shortName="T")
  public String TAG

• TAG_VALUE

  @Argument(doc="The tag value(s) to filter by",
            optional=true,
            shortName="TV")
  public List<String> TAG_VALUE

• SORT_ORDER

  @Argument(doc="SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file.",
            optional=true,
            shortName="SO")
  public htsjdk.samtools.SAMFileHeader.SortOrder SORT_ORDER

• OUTPUT

  @Argument(doc="SAM or BAM file for resulting reads.",
            shortName="O")
  public File OUTPUT

• JAVASCRIPT_FILE

  @Argument(shortName="JS",
            doc="Filters the INPUT with a javascript expression using the java javascript-engine, when using FILTER=includeJavascript.  The script puts the following variables in the script context: \n \'record\' a SamRecord ( https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and \n  \'header\' a SAMFileHeader ( https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ).\n all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted if the last value of the script evaluates to true.",
            optional=true)
  public File JAVASCRIPT_FILE

• WRITE_READS_FILES

  @Argument(doc="Create <OUTPUT>.reads file containing names of reads from INPUT and OUTPUT (for debugging purposes.)",
            optional=true)
  public boolean WRITE_READS_FILES

Constructor Detail

• FilterSamReads

  public FilterSamReads()

Method Detail

• 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 class CommandLineProgram

  Returns:

  program exit status.

• customCommandLineValidation

  protected String[] customCommandLineValidation()

  Description copied from class: CommandLineProgram
  Put any custom command-line validation in an override of this method. clp is initialized at this point and can be used to print usage and access argv. Any options set by command-line parser can be validated.

  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.