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_compress_reads(1) sand_uncompress_reads(1) work_queue_worker(1)