Package picard.sam

Class ViewSam


  • @DocumentedFeature
    public class ViewSam
    extends CommandLineProgram
    Prints a SAM or BAM file to the screen.

    Very simple command that just reads a SAM or BAM file and writes out the header and each record to standard out. When an (optional) intervals file is specified, only records overlapping those intervals will be output.

    All reads, just the aligned reads, or just the unaligned reads can be printed out by setting AlignmentStatus accordingly. The SAM or BAM header can be printed out separately using HEADER_ONLY. Only the alignment records can be printed using RECORDS_ONLY. However, HEADER_ONLY and RECORDS_ONLY cannot both be specified at one time.

    Inputs

    • A SAM or BAM file to be viewed
    • Optional arguments specifying which reads or records need to be viewed

    Usage example:

         java -jar picard.jar ViewSam \
              I=input_reads.bam \
              HEADER_ONLY=true
     


    • Field Detail

      • USAGE

        public final String USAGE
      • INPUT

        @Argument(shortName="I",
                  doc="The SAM or BAM file or GA4GH url to view.")
        public String INPUT
      • ALIGNMENT_STATUS

        @Argument(doc="Print out all reads, just the aligned reads or just the unaligned reads.")
        public ViewSam.AlignmentStatus ALIGNMENT_STATUS
      • PF_STATUS

        @Argument(doc="Print out all reads, just the PF reads or just the non-PF reads.")
        public ViewSam.PfStatus PF_STATUS
      • HEADER_ONLY

        @Argument(doc="Print the SAM header only.",
                  optional=true)
        public boolean HEADER_ONLY
      • RECORDS_ONLY

        @Argument(doc="Print the alignment records only.",
                  optional=true)
        public boolean RECORDS_ONLY
      • INTERVAL_LIST

        @Argument(doc="An intervals file used to restrict what records are output.",
                  optional=true)
        public File INTERVAL_LIST
    • Constructor Detail

      • ViewSam

        public ViewSam()
    • 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.