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gt-chain2dim - Chain pairwise matches.


gt chain2dim [options] -m matchfile


-m [filename]
Specify file containing the matches mandatory option (default: undefined)

perform global chaining

· optional parameter gc switches on gap costs (according to L1-model)

· optional parameter ov means that overlaps between matches are allowed

· optional parameter all means that all optimal chains are processed

perform local chaining compute local chains (according to L1-model).

· If no parameter is given, compute local chains with maximums 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

· If a number is followed by character b, then output all chains with the largest k

· If a number is followed by character p, then output all chains with scores at most
k percent away from the best score.

-wf [value]
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)

-maxgap [value]
specify maximal width of gap in chain (default: 0)

-silent [yes|no]
do not output the chains but only report their lengths and scores (default: no)

-v [yes|no]
be verbose (default: no)

display help and exit

display version information and exit


Report bugs to <kurtz@zbh.uni-hamburg.de>.

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