sand_compress_reads

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)