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

.SH NAME
.LP
\fBsand_align_kernel\fP - align candidate sequences sequentially

.SH SYNOPSIS
.LP
\FC\fBsand_align_kernel [options] [input file]\fP\FT

.SH DESCRIPTION
.LP

\fBsand_align_kernel\fP aligns candidate sequences sequentially.
It is not normally called by the user, but is invoked by
\fBsand_align_master(1)\fP for each sequential step of a distributed
alignment workload.  The options to \fBsand_align_kernel\fP control
the type of alignment (Smith-Waterman, Prefix-Suffix, Banded, etc)
and the quality threshhold for reporting alignments.  These options
are typically passed in by giving the \fB-e\fP option to \fBsand_align_master\fP.
.PP
\fBsand_align_kernel\fP reads a list of sequences
from the given input file, or from standard input if none is given.
The sequences are in the compressed fasta format produced
by \fBsand_compress_reads(1)\fP.  The first sequence in the input
is compared against all following sequences until a separator line.
Following the separator, the next sequence is compared against
all following sequences until the following separator, and so on.

.SH OPTIONS
.LP

.LP
.TP
.BI \ -a \ <sw|ps|banded>
.
Specify the type of alignment: sw (Smith-Waterman), ps (Prefix-Suffix), or banded.  If not specified, default is banded.
.TP
.BI \ -o \ <ovl|ovl_new|align|matrix>
.
Specify how each alignment should be output: ovl (Celera V5, V6 OVL format), ovl_new (Celera V7 overlap format), align (display the sequences and alignment graphically) or matrix (display the dynamic programming matrix).  \fBsand_align_master(1)\fP expects the ovl output format, which is the default.  The other formats are useful for debugging.
.TP
.BI \ -m \ <length>
.
Minimum aligment length (default: 0).
.TP
.BI \ -q \ <quality>
.
Minimum match quality (default: 1.00)
.TP
.B \ -x
.
Delete input file after completion.
.TP
.BI \ -d \ <subsystem>
.
Enable debugging for this subsystem.  (Try \fB-d all\fP to start.
.TP
.B \ -v
.
Show program version.
.TP
.B \ -h
.
Display this message.


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

.SH EXAMPLES
.LP

Users do not normally invoke sand_align_kernel directly.  Instead, pass arguments by using the \fB-e\fP option to \fBsand_align_master(1)\fP.  For example, to specify a minimum alignment length of 5 and a minimum quality of 0.25:

.fam C
.nf
.nh
.IP "" 8
% sand_align_master sand_align_kernel -e "-m 5 -q 0.25" mydata.cand mydata.cfa mydata.ovl
.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