substitch.pl1
Usage
substitch.pl --split
5
allchromosomes.stitch
#split
big
stitch
into
5
roughly
equal
chunks
substitch.pl --project
allspecies.seqs
sub.anchors
#project
some
anchors
into
a
different
coordinate
space
(as
long
as
the
stitch
component
sequences
match)
Options
--verbose => makes more verbose --faketfidf => fake tfidf scores based on score stat in file
Note on split: This program does not claim to produce an optimal splitting. It tries a couple heuristics, refines the results, and picks the best arrangement it's found so far. Technically this is a variation on the traditional "trunk packing problem," which is (at least in the abstract case) NP-hard, if I remember 15-251 correctly. This particular variety of trunk packing however, seems like it should be solvable faster (worst case some n^k dynamic programming I think, but I'm betting this way is faster and tons easier to write for 90% of the cases out there). If anyone reading this goes "You moron, this has been solved a thousand times already," please let me know how: [email protected]
Releases
5 releases since Debian 9 (Stretch); the text changed 4 times.