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)