added trimming of scores to remove_adaptor

git-svn-id: http://biopieces.googlecode.com/svn/trunk@947 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/remove_adaptor b/bp_bin/remove_adaptor
index 14a7f896d46e9cbb23d2e6c6256bd2623964c3e3..3edf3ac4fa749eabe34fff8d643a5f57f1a7f209 100755 (executable)
--- a/bp_bin/remove_adaptor
+++ b/bp_bin/remove_adaptor
@@ -77,12 +77,14 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
         {
             if ( $options->{ "remove" } eq "after" )
             {
-                $record->{ "SEQ" }     = substr $record->{ "SEQ" }, 0, $pos;
+                $record->{ "SEQ" }     = substr $record->{ "SEQ" },    0, $pos;
+                $record->{ "SCORES" }  = substr $record->{ "SCORES" }, 0, $pos;
                 $record->{ "SEQ_LEN" } = $pos;
             }
             else
             {
-                $record->{ "SEQ" }     = substr $record->{ "SEQ" }, $pos + $adaptor_len;
+                $record->{ "SEQ" }     = substr $record->{ "SEQ" },    $pos + $adaptor_len;
+                $record->{ "SCORES" }  = substr $record->{ "SCORES" }, $pos + $adaptor_len;
                 $record->{ "SEQ_LEN" } = length $record->{ "SEQ" };
             }
         }

diff --git a/bp_bin/swapcase_seq b/bp_bin/swapcase_seq
index 62a69796b04e50b53ab529fd951e7db976d21758..997d948ecc0affbd8e595ec800c13e0e298121e1 100755 (executable)
--- a/bp_bin/swapcase_seq
+++ b/bp_bin/swapcase_seq
@@ -24,7 +24,7 @@ optparse = OptionParser.new do |opts|
 #              options[:stream_in] = arg
 #      end
 
-       opts.on( '-O', '--stream_in FILE', "Mandatory argument" ) do |arg|
+       opts.on( '-O', '--stream_out FILE', "Mandatory argument" ) do |arg|
                options[:stream_out] = arg
        end
 end