X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Fremove_adaptor;h=c709b4f1cd11d2fd13814885adeb416eba12c3dd;hb=48bea5c28b89dc5586d0bddb338ccd6ba23aa1f9;hp=f037055ad08e6a840830eca2e31ae5f396b0a289;hpb=5aed4676ad1bf35abbade6215ac90ee591e6d8fe;p=biopieces.git

diff --git a/bp_bin/remove_adaptor b/bp_bin/remove_adaptor
index f037055..c709b4f 100755
--- a/bp_bin/remove_adaptor
+++ b/bp_bin/remove_adaptor
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Common;
@@ -76,12 +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" };
             }
         }