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.IX Title "SUBSTITCH 1"
.TH SUBSTITCH 1 2024-11-09 "perl v5.40.0" "User Contributed Perl Documentation"
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.SH NAME
substitch.pl \-\- Split/merge stitch files into/out of stitch files
.SH SYNOPSIS
.IX Header "SYNOPSIS"
substitch.pl \-\-split 5 allchromosomes.stitch  #split big stitch into 5 roughly equal chunks
.PP
substitch.pl \-\-project allspecies.seqs sub.anchors #project some anchors into a different coordinate space (as long as the stitch component sequences match)
.SH OPTIONS
.IX Header "OPTIONS"
\&\-\-verbose => makes more verbose
\&\-\-faketfidf => fake tfidf scores based on score stat in file
.PP
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