X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Falign_seq;h=af114e1da2d78e1490cbf016fc10ab89a4656fe1;hb=0411353f55e9af778a3e1390a430970fed0ce971;hp=e34759a9c34472058382d2587faf567904a2ef56;hpb=52cd51e0b58ed81c412770c2e458838603c2d2ad;p=biopieces.git

diff --git a/bp_bin/align_seq b/bp_bin/align_seq
index e34759a..af114e1 100755
--- a/bp_bin/align_seq
+++ b/bp_bin/align_seq
@@ -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::Align;
@@ -39,7 +40,7 @@ use constant {
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, @entries, $entry );
+my ( $options, $in, $out, $record, @entries, $entry );
 
 $options = Maasha::Biopieces::parse_options();
 
@@ -66,32 +67,29 @@ foreach $entry ( @entries )
         $record = {
             SEQ_NAME => $entry->[ SEQ_NAME ],
             SEQ      => $entry->[ SEQ ],
+            SEQ_LEN  => length $entry->[ SEQ ],
         };
 
         Maasha::Biopieces::put_record( $record, $out );
     }
 }
 
+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();
 }
 
 
@@ -99,4 +97,3 @@ END
 
 
 __END__
-