'\" t
.\"     Title: chain2dim
.\"    Author: [see the "AUTHOR(S)" section]
.\" Generator: Asciidoctor 2.0.16
.\"      Date: 
.\"    Manual: \ \&
.\"    Source: \ \&
.\"  Language: English
.\"
.TH "CHAIN2DIM" "1" "" "\ \&" "\ \&"
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.SH "NAME"
chain2dim \- two\-dimensional match chaining
.SH "SYNOPSIS"
.sp
\fBchain2dim\fP [options] <matchfile>
.SH "OPTIONS"
.sp
\fB\-global\fP <param>
.RS 4
Global chaining. Optional parameter "gc" switches on gap costs (according to
L1\-model). Optional parameter "ov" means that overlaps between matches are
allowed.
.RE
.sp
\fB\-local\fP <param>
.RS 4
Compute local chains (according to L1\-model).
If no parameter is given, compute local chains with maximum score.
If parameter is given, this must be a positive number optionally followed by
the character b or p. If only the number, say k, is given, this is the
minimum score of the chains output.
If a number is followed by character b, then output all chains with the
largest k scores. If a number is followed by character p, then output all
chains with scores at most k percent away from the best score.
.RE
.sp
\fB\-wf\fP <factor>
.RS 4
Specify weight factor > 0.0 to obtain the score of a fragment. Requires one
of the options \fB\-local\fP, \fB\-global gc\fP or \fB\-global ov\fP.
.RE
.sp
\fB\-maxgap\fP <width>
.RS 4
Maximal width of gap in chain.
.RE
.sp
\fB\-outprefix\fP <prefix>
.RS 4
Specify prefix of files to output chains.
.RE
.sp
\fB\-withinborders\fP
.RS 4
Only compute chains which do not cross sequence borders (not possible for
matches in open format).
.RE
.sp
\fB\-thread\fP <keywords...>
.RS 4
Thread the chains, i.e. close the gaps. Accepts an optional list of keywords
"minlen1 minlen2 maxerror1 maxerror2", each followed by a number specifies
the minimum length and the maximum error rate of thread.
1 refers to match instance in indexed sequence, 2 refers to matching
instance in query.
.RE
.sp
\fB\-silent\fP
.RS 4
Do not output the chains and only report their lengths and scores.
.RE
.sp
\fB\-v\fP
.RS 4
Be verbose.
.RE
.sp
\fB\-version\fP
.RS 4
Show the version of the Vmatch package.
.RE
.sp
\fB\-help\fP
.RS 4
Show help.
.RE
.SH "SEE ALSO"
.sp
vmatch(1)