fixed bug in assemble_pairs

[biopieces.git] / bp_bin / assemble_pairs

diff --git a/bp_bin/assemble_pairs b/bp_bin/assemble_pairs
index a101f3e16d0b0f09aa2f9dd9380c44bb1ef46231..df1fd0320a94d218e187067e4af03f5ba9436849 100755 (executable)
--- a/bp_bin/assemble_pairs
+++ b/bp_bin/assemble_pairs
@@ -54,9 +54,9 @@ def names_match(entry1, entry2)
 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=>1,   :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)
 
@@ -84,16 +84,17 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
           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
             new_record = merged.to_bp
 
-            if merged.seq_name =~ /overlap=(\d+)$/
-              new_record[:OVERLAP_LEN] = $1
+            if merged.seq_name =~ /overlap=(\d+):hamming=(\d+)$/
+              new_record[:OVERLAP_LEN]  = $1
+              new_record[:HAMMING_DIST] = $2
             end
 
             output.puts new_record