VERSION 0.66
---------------------------------------------------------------------
fixed a section of code in masking logic which would cause a warning
if user got no hits to their masking database.

VERSION 0.65
---------------------------------------------------------------------
added the ability to get the coordinates back from a mask.
usually mask is called in a scalar context, but if you ask 
in an array context you will receive a masked sequence and
a reference to an array of masked sequences.

VERSION 0.64 (never released)
---------------------------------------------------------------------
Version .63 fix fixed a masking problem but introduced a bug in blasting
which would delete all BLAST reports after BLASTing.  (version .63 was
never released).  This version re-fixes the masking problem without 
breaking anything else.

VERSION 0.63 (never released)
---------------------------------------------------------------------
fixed problem with masking in which masking would fail if you provided -o opt
fixed typo in pod documentation.

VERSION 0.61
---------------------------------------------------------------------
fixed pod which caused make to gripe
fixed reference in README

VERSION 0.60
---------------------------------------------------------------------
added bl2seq method which BLASTs 2 sequences against each other
added blast_one_to_many method which BLASTs 1 sequence against
  a library of sequences.
added formatdb method which creates BLASTable databases
added remove_formatdb_indexes method which removes the BLASTable
  databases made by the formatdb method.
cleaned up some of the code
fixed a couple methods so they would work with other methods besides blastall
updated documentation

VERSION 0.56
---------------------------------------------------------------------
added get_report method which returns the BLAST report file.

VERSION 0.55
---------------------------------------------------------------------
fixes a bug which would turn some 0.0 expect values to 1000
if they did not appear in the summaries.  This was to correct 
an old bug in NCBI BLAST but seems to not exist any longer.

VERSION 0.54
---------------------------------------------------------------------
added the blastcl3 method which uses the blastcl3 binary
to make network BLASTs.  This became necessary when NCBI
changed their web interface (QBLAST) and broke my LWP 
routines.

VERSION 0.53
---------------------------------------------------------------------
fixed bug in wu-blast option processing.

VERSION 0.52
---------------------------------------------------------------------
Added check to make sure temporary directories are writable.

VERSION 0.51
---------------------------------------------------------------------
Added query_ends and subject_ends to the data parsed from the BLAST report
instead of relying on query_starts and match_lengths to get the end.

VERSION 0.50
---------------------------------------------------------------------
fixed a number of bugs.  Added the DB_ID_REGEX
added some accessor methods to get the database description,
number of sequences in the database, number of letters in the database,
BLAST program and program version.

VERSION 0.44
---------------------------------------------------------------------

Blastall now parses and stores "Frames" from blastx, tblastn and tblastx runs.
Updated documentation.

VERSION 0.43
---------------------------------------------------------------------

fixed some misleading documentation

VERSION 0.42
----------------------------------------------------------------------

methods that required a hash_ref (wu-blastall, blastall, net-blastall and mask)
will now accept a hash.  so you can either say...

    blastall({'p'=>'blastn', 'd'=>'nr', 'i'=>'infile'});  #with ref
    blastall('p'=>'blastn', 'd'=>'nr', 'i'=>'infile');    #without ref

Fixed the test suite so it tests for LWP modules before trying to run
net-blastall.  If it doesn't find LWP modules it looks for $BLASTDB
environmental variable.  If your BLASTDB environmental variable =~ /wu/
than it will run wu-blastall.  If the BLASTDB env var does exist but
does not have the 'wu' pattern it tries to run NCBI's BLAST via the
blastall method.  If all else fails it gives you a warning and fails
the test.


VERSION 0.41
----------------------------------------------------------------------
Filter method used to remove sub entries but now does not.
Now if query sequence has one significant hit to a subject sequence
    all hits to that sequence are shown.
There is a bug(feature?).  
    If one of the hits passes on Identity but not E-value
    and another hit does the opposite all hits are reported. 
    Haven't decided what to do about this.

NEW IN VERSION 0.40
----------------------------------------------------------------------
* support for WU BLAST
* support for WWW BLAST through NCBI
  HOWEVER: NCBI has recently changed there web protocol to QBLAST and this
  may present future problems.
* added sample scripts in scripts directory for WU, WWW and NCBI BLASTs
* documentation may be slightly behind.  Sorry.  Working on this...

