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Description
- blast each feature against the databases, store in a map from feature name to a list of matches with that feature
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traverse the ordered list of features and find the minimum cost/length combinations of fragments/vectors to assemble a vector with all the features in order(returning all solutions) -
add dbs flag to 'defrag features find' allow checking of features in databases as wellwill add 'defrag ls fragment [name]' instead - return pareto optimal solutions
Feature CLI Grammar
[name]:fwd/rev:l#:r#
- fwd/rev = whether it's in fwd or rev direction, fwd assumed
- l# = upper bound on "padding" in bp to consume from the left matched fragment
- r# = upper bound on "padding" in bp to consume from the right matched fragment
default l/r is unlimited for matches that contain adjacent features and 0 for matches without any other additional features
Longterm
- read in Genbank file features and use
- read in multi-FASTA file features
- gap penalty for inserting a new feature? Post assembly, blast each vector solution against the features db and penalize those that added new features
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