Provided by: vmatch_2.3.1+dfsg-8_amd64
chain2dim - two-dimensional match chaining
chain2dim [options] <matchfile>
-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.