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) 2022 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_com‐
           press_reads(1)  sand_uncompress_reads(1)  work_queue_worker(1)

CCTools 7.14.5 FINAL                                                                      sand_compress_reads(1)