NAME

       substitch.pl -- Split/merge stitch files into/out of stitch files

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: krisp@dna.bio.keio.ac.jp