From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Wed, 13 Mar 2013 09:25:30 +0000 (+0000)
Subject: fixed defaults and key names
X-Git-Url: https://git.donarmstrong.com/?p=biopieces.git;a=commitdiff_plain;h=dacbae7a2e1355bc1f2e30a839a7fe7574f306f0

fixed defaults and key names

git-svn-id: http://biopieces.googlecode.com/svn/trunk@2138 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/bp_bin/assemble_pairs2 b/bp_bin/assemble_pairs2
index f6d2f28..3741222 100755
--- a/bp_bin/assemble_pairs2
+++ b/bp_bin/assemble_pairs2
@@ -35,7 +35,7 @@ require 'maasha/seq/assemble'
 require 'pp'
 
 casts = []
-casts << {:long=>'mismatches',  :short=>'m', :type=>'uint', :mandatory=>false, :default=>10,  :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'mismatches',  :short=>'m', :type=>'uint', :mandatory=>false, :default=>5,   :allowed=>nil, :disallowed=>nil}
 casts << {:long=>'overlap_min', :short=>'o', :type=>'uint', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>"0"}
 casts << {:long=>'overlap_max', :short=>'p', :type=>'uint', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>"0"}
 
@@ -68,7 +68,7 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
           new_record = merged.to_bp
 
           if merged.seq_name =~ /overlap=(\d+):hamming=(\d+)$/
-            new_record[:OVERLAP]      = $1
+            new_record[:OVERLAP_LEN]  = $1
             new_record[:HAMMING_DIST] = $2
           end