'\" t
.\"     Title: gt-chain2dim
.\"    Author: [FIXME: author] [see http://www.docbook.org/tdg5/en/html/author]
.\" Generator: DocBook XSL Stylesheets vsnapshot <http://docbook.sf.net/>
.\"      Date: 07/22/2020
.\"    Manual: GenomeTools Manual
.\"    Source: GenomeTools 1.6.1
.\"  Language: English
.\"
.TH "GT\-CHAIN2DIM" "1" "07/22/2020" "GenomeTools 1\&.6\&.1" "GenomeTools Manual"
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.SH "NAME"
gt-chain2dim \- Chain pairwise matches\&.
.SH "SYNOPSIS"
.sp
\fBgt chain2dim\fR [options] \-m matchfile
.SH "DESCRIPTION"
.PP
\fB\-m\fR [\fIfilename\fR]
.RS 4
Specify file containing the matches mandatory option (default: undefined)
.RE
.PP
\fB\-global\fR
.RS 4
perform global chaining
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
optional parameter gc switches on gap costs (according to L1\-model)
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
optional parameter ov means that overlaps between matches are allowed
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
optional parameter all means that all optimal chains are processed
.RE
.RE
.PP
\fB\-local\fR
.RS 4
perform local chaining compute local chains (according to L1\-model)\&.
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
If no parameter is given, compute local chains with maximums score\&.
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
If parameter is given, this must be a positive number optionally followed by the character b or p\&.
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
If only the number, say k, is given, this is the minimum score of the chains output\&.
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
If a number is followed by character b, then output all chains with the largest k scores\&.
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
If a number is followed by character p, then output all chains with scores at most k percent away from the best score\&.
.RE
.RE
.PP
\fB\-wf\fR [\fIvalue\fR]
.RS 4
specify weight factor > 0\&.0 to obtain score of a fragment requires one of the options \-local const \-global gc \-global ov (default: 1\&.000000)
.RE
.PP
\fB\-maxgap\fR [\fIvalue\fR]
.RS 4
specify maximal width of gap in chain (default: 0)
.RE
.PP
\fB\-silent\fR [\fIyes|no\fR]
.RS 4
do not output the chains but only report their lengths and scores (default: no)
.RE
.PP
\fB\-v\fR [\fIyes|no\fR]
.RS 4
be verbose (default: no)
.RE
.PP
\fB\-help\fR
.RS 4
display help and exit
.RE
.PP
\fB\-version\fR
.RS 4
display version information and exit
.RE
.SH "REPORTING BUGS"
.sp
Report bugs to <kurtz@zbh\&.uni\-hamburg\&.de>\&.