SYNOPSIS

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]