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