CHAIN2DIM(1)

NAME
chain2dim - two-dimensional match chaining

SYNOPSIS

chain2dim [options] <matchfile>

OPTIONS

-global <param>
    Global chaining. Optional parameter "gc" switches on gap costs (according to L1-model). Optional parameter "ov" means that overlaps between matches are allowed.

-local <param>
    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.

-wf <factor>
    Specify weight factor > 0.0 to obtain the score of a fragment. Requires one of the options -local, -global gc or -global ov.

-maxgap <width>
    Maximal width of gap in chain.

-outprefix <prefix>
    Specify prefix of files to output chains.

-withinborders
    Only compute chains which do not cross sequence borders (not possible for matches in open format).

-thread <keywords...>
    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.

-silent
    Do not output the chains and only report their lengths and scores.

-v
    Be verbose.

-version
    Show the version of the Vmatch package.

-help
    Show help.

SEE ALSO

vmatch(1)