reverted findsim_seq and renamed precise switch to realign

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1817 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/findsim_seq b/bp_bin/findsim_seq
index f12a18811655e51e1497f6bea74eb6060e3b98a4..fec7772269aed40b6fd0bccde1bf1b9a78faeaa3 100755 (executable)
--- a/bp_bin/findsim_seq
+++ b/bp_bin/findsim_seq
@@ -41,7 +41,7 @@ casts << {:long=>'min_score',   :short=>'m', :type=>'float', :mandatory=>false,
 casts << {:long=>'max_hits',    :short=>'h', :type=>'uint',  :mandatory=>false, :default=>7,   :allowed=>nil,           :disallowed=>"0"}
 casts << {:long=>'query_ids',   :short=>'Q', :type=>'flag',  :mandatory=>false, :default=>nil, :allowed=>nil,           :disallowed=>nil}
 casts << {:long=>'subject_ids', :short=>'S', :type=>'flag',  :mandatory=>false, :default=>nil, :allowed=>nil,           :disallowed=>nil}
-casts << {:long=>'precise',     :short=>'p', :type=>'flag',  :mandatory=>false, :default=>nil, :allowed=>nil,           :disallowed=>nil}
+casts << {:long=>'realign',     :short=>'r', :type=>'flag',  :mandatory=>false, :default=>nil, :allowed=>nil,           :disallowed=>nil}
 
 options    = Biopieces.options_parse(ARGV, casts)
 tmpdir     = Biopieces.mktmpdir