From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Tue, 20 Apr 2010 15:21:55 +0000 (+0000)
Subject: added trimming of scores to remove_adaptor
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=5487798582369ff097f489d3f65b1baa5766b17c;p=biopieces.git

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 14a7f89..3edf3ac 100755
--- 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 62a6979..997d948 100755
--- 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