maf-cull
========

This script aims to "cull" redundant alignments.  It removes
alignments whose coordinates in the top-most sequence are contained in
LIMIT or more higher-scoring alignments.

Alignments using opposite strands of the top-most sequence are not
considered to contain each other.

The alignments must have been sorted beforehand by maf-sort.  If not,
maf-cull will quit with an error message.

You can use it like this::

  maf-cull --limit=3 sorted-alignments.maf > culled.maf
  maf-cull -l3 sorted-alignments.maf > culled.maf

If you want to cull based on a sequence other than the top one, use
maf-swap to bring that sequence to the top.

This type of culling can also be done by NCBI BLAST, and it is
described in this article:

  Winnowing sequences from a database search.
  Berman P, Zhang Z, Wolf YI, Koonin EV, Miller W.
  J Comput Biol. 2000 7:293-302.

Options
-------

  -h, --help                  Print a help message and exit.
  -l LIMIT, --limit=LIMIT     Set the culling limit to LIMIT.