fixed seq qual length check

[biopieces.git] / bp_bin / remove_adaptor

diff --git a/bp_bin/remove_adaptor b/bp_bin/remove_adaptor
index 118bab32f6636cee4ff22e6fec72babde6874fd8..c709b4f1cd11d2fd13814885adeb416eba12c3dd 100755 (executable)
--- a/bp_bin/remove_adaptor
+++ b/bp_bin/remove_adaptor
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl -w
+#!/usr/bin/env perl
 
 # Copyright (C) 2007-2009 Martin A. Hansen.
 
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Common;
@@ -34,7 +35,7 @@ use Maasha::Common;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $adaptor, $seq, $adaptor_len,
+my ( $options, $in, $out, $record, $adaptor, $seq, $adaptor_len,
      $seq_len, $offset, $max_match, $max_mismatch, $pos );
 
 $options = Maasha::Biopieces::parse_options(
@@ -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" };
             }
         }
@@ -94,26 +97,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     }
 }
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
 
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -121,4 +120,3 @@ END
 
 
 __END__
-