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GT-CHAIN2DIM(1) GenomeTools Manual GT-CHAIN2DIM(1)

NAME

gt-chain2dim - Chain pairwise matches.

SYNOPSIS

gt chain2dim [options] -m matchfile

DESCRIPTION

-m [filename]
Specify file containing the matches mandatory option (default: undefined)
-global
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
-local
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 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 [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)
-help
display help and exit
-version
display version information and exit

REPORTING BUGS

Report bugs to <kurtz@zbh.uni-hamburg.de>.
09/05/2014 GenomeTools 1.5.3