.TH "sand_compress_reads" 1 "" "CCTools 7.1.2 FINAL" "Cooperative Computing Tools"

.SH NAME
.LP
\fBsand_compress_reads\fP - compress sequence data

.SH SYNOPSIS
.LP
\FC\fBsand_compress_reads [-qcivh] [infile] [outfile]\fP\FT

.SH DESCRIPTION
.LP

\fBsand_compress_reads\fP reads sequence data in standard FASTA format,
and produces output in the compressed FASTA (cfa) format used by
the \fBsand_filter_master(1)\fP and \fBsand_align_master(1)\fP.
.PP
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.

.SH OPTIONS
.LP

.LP
.TP
.B \ -q
.
Quiet mode: suppress summary line.
.TP
.B \ -c
.
Remove Celera read ids if data came from the Celera gatekeeper.
.TP
.B \ -i
.
Remove Celera read ids but leave internal ids if the data came from the Celera gatekeeper.
.TP
.B \ -h
.
Display version information.
.TP
.B \ -v
.
Show help text.


.SH EXIT STATUS
.LP
On success, returns zero.  On failure, returns non-zero.

.SH EXAMPLES
.LP

To compress \FCmydata.fasta\FT into \FCmydata.cfa\FT:

.fam C
.nf
.nh
.IP "" 8
% sand_compress_reads mydata.fasta mydata.cfa
.fi
.hy
.fam
.P

.SH COPYRIGHT
.LP

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.

.SH SEE ALSO
.LP


.IP \(bu 4
\fBCooperative Computing Tools Documentation\fP
.IP \(bu 4
\fBSAND User Manual\fP
.IP \(bu 4
\fBsand_filter_master(1)\fP  \fBsand_filter_kernel(1)\fP  \fBsand_align_master(1)\fP  \fBsand_align_kernel(1)\fP  \fBsand_compress_reads(1)\fP  \fBsand_uncompress_reads(1)\fP  \fBwork_queue_worker(1)\fP