Field Detail

• INPUT

  @Option(shortName="I",
          doc="Input SAM or BAM file.")
  public File INPUT

• OUTPUT

  @Option(shortName="O",
          doc="File to write the output to.")
  public File OUTPUT

• ASSUME_SORTED

  @Option(doc="If true (default), then the sort order in the header file will be ignored.",
          shortName="AS")
  public boolean ASSUME_SORTED

• STOP_AFTER

  @Option(doc="Stop after processing N reads, mainly for debugging.")
  public long STOP_AFTER

Constructor Detail

• SinglePassSamProgram

  public SinglePassSamProgram​()

Method Detail

• doWork

  protected final int doWork​()

  Final implementation of doWork() that checks and loads the input and optionally reference sequence files and the runs the sublcass through the setup() acceptRead() and finish() steps.

  Specified by:

  doWork in class CommandLineProgram

  Returns:

  program exit status.

• makeItSo

  public static void makeItSo​(File input,
                              File referenceSequence,
                              boolean assumeSorted,
                              long stopAfter,
                              Collection<SinglePassSamProgram> programs)

• usesNoRefReads

  protected boolean usesNoRefReads​()

  Can be overriden and set to false if the section of unmapped reads at the end of the file isn't needed.

• setup

  protected abstract void setup​(htsjdk.samtools.SAMFileHeader header,
                                File samFile)

  Should be implemented by subclasses to do one-time initialization work.

• acceptRead

  protected abstract void acceptRead​(htsjdk.samtools.SAMRecord rec,
                                     htsjdk.samtools.reference.ReferenceSequence ref)

  Should be implemented by subclasses to accept SAMRecords one at a time. If the read has a reference sequence and a reference sequence file was supplied to the program it will be passed as 'ref'. Otherwise 'ref' may be null.

• finish

  protected abstract void finish​()

  Should be implemented by subclasses to do one-time finalization work.