adding bzip2 support in ruby

[biopieces.git] / bp_bin / remove_adaptor

diff --git a/bp_bin/remove_adaptor b/bp_bin/remove_adaptor
index 14a7f896d46e9cbb23d2e6c6256bd2623964c3e3..c709b4f1cd11d2fd13814885adeb416eba12c3dd 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 if $record->{ "SCORES" };
                 $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 if $record->{ "SCORES" };
                 $record->{ "SEQ_LEN" } = length $record->{ "SEQ" };
             }
         }