NAME

       sand_compress_reads - compress sequence data

SYNOPSIS

       sand_compress_reads [-qcivh] [infile] [outfile]

DESCRIPTION

       sand_compress_reads  reads  sequence data in standard FASTA format, and produces output in
       the   compressed   FASTA   (cfa)   format   used   by   the   sand_filter_master(1)    and
       sand_align_master(1).

       If  the  output  file  is omitted, standard output is used.  if the input file is omitted,
       standard input is used.  After completing the compression,  this  program  will  output  a
       summary line of sequences and bytes compressed.

OPTIONS

        -q    Quiet mode: suppress summary line.

        -c    Remove Celera read ids if data came from the Celera gatekeeper.

        -i    Remove  Celera  read  ids  but  leave internal ids if the data came from the Celera
              gatekeeper.

        -h    Display version information.

        -v    Show help text.

EXIT STATUS

       On success, returns zero.  On failure, returns non-zero.

EXAMPLES

       To compress mydata.fasta into mydata.cfa:

               % sand_compress_reads mydata.fasta mydata.cfa

COPYRIGHT

       The Cooperative Computing Tools are Copyright (C) 2005-2019 The University of Notre  Dame.
       This  software  is distributed under the GNU General Public License.  See the file COPYING
       for details.

SEE ALSO

       •   Cooperative Computing Tools Documentation

       •   SAND User Manual

       •   sand_filter_master(1)            sand_filter_kernel(1)            sand_align_master(1)
           sand_align_kernel(1)          sand_compress_reads(1)          sand_uncompress_reads(1)
           work_queue_worker(1)