end
casts = []
-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"}
+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: 1, allowed: nil, disallowed: "0"}
+casts << {long: 'overlap_max', short: 'p', type: 'uint', mandatory: false, default: nil, allowed: nil, disallowed: "0"}
options = Biopieces.options_parse(ARGV, casts)
merged = Assemble.pair(
entry1,
entry2,
- mismatches_max:options[:mismatches],
- overlap_min:options[:overlap_min],
- overlap_max:options[:overlap_max]
+ mismatches_max: options[:mismatches],
+ overlap_min: options[:overlap_min],
+ overlap_max: options[:overlap_max]
)
if merged