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sand_compress_reads(1) Cooperative Computing Tools sand_compress_reads(1)

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

CCTools 7.2.0 FINAL