novo2maq
--------
Novo2maq is a utility based on maq code that converts output reports from Novoalign V2 & V1 to MAQ map format
It is based on MAQ code and distributed under MAQ license. This release includes some fixes and Novoalign V2.0
compatability that are not in the maq version.

Make

A Makefile is provided that should work with most Linux systems.


Use 'make' and manually copy the novo2maq executables to the destination directory.
Modification to 'Makefile' is sometimes needed for different architectures.


MAQ Version 0.7.x vs maq 0.6.x
------------------------------

By default novo2maq is compiled to be compatible with relesae 0.7.1 of Maq. If you
require maq 0.6.8 compatability delete the line

DFLAGS= -D_FASTMAP -DMAQ_LONGREADS

from the Makefile

Change History
--------------
15th February 2009
 Fix a problem when converting output from novoalign with the -m option set (miRNA hairpin score)
