fixed seq qual length check

[biopieces.git] / bp_bin / write_2bit

diff --git a/bp_bin/write_2bit b/bp_bin/write_2bit
index 1a1f756d570ef833b72512b72514ddc40830d4a9..12e330dbbd872bddc468bc8361d36d6152502b34 100755 (executable)
--- a/bp_bin/write_2bit
+++ b/bp_bin/write_2bit
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl -w
+#!/usr/bin/env perl
 
 # Copyright (C) 2007-2009 Martin A. Hansen.
 
@@ -29,6 +29,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Fasta;
 use Maasha::Biopieces;
@@ -39,7 +40,7 @@ use Maasha::TwoBit;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $mask, $tmp_dir, $tmp_file, $fh_tmp, $fh_in, $fh_out, $entry );
+my ( $options, $in, $out, $record, $mask, $tmp_dir, $tmp_file, $fh_tmp, $fh_in, $fh_out, $entry );
 
 $options = Maasha::Biopieces::parse_options(
     [
@@ -82,7 +83,8 @@ close $fh_out;
 
 unlink $tmp_file;
 
-Maasha::Filesys::dir_remove( $tmp_dir );
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
 
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
@@ -90,19 +92,13 @@ Maasha::Filesys::dir_remove( $tmp_dir );
 
 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();
 }