removed debug message

[biopieces.git] / bp_bin / read_soft

diff --git a/bp_bin/read_soft b/bp_bin/read_soft
index f83aab7a1096804559bcd6e226c1a1c95881c7f2..10ae8c1bb405914db2d0c83c5e6a343de7a79ca1 100755 (executable)
--- a/bp_bin/read_soft
+++ b/bp_bin/read_soft
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl -w
+#!/usr/bin/env perl
 
 # Copyright (C) 2007-2009 Martin A. Hansen.
 
@@ -27,7 +27,9 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
+use Data::Dumper;
 use Maasha::Biopieces;
 use Maasha::Filesys;
 use Maasha::NCBI;
@@ -36,7 +38,7 @@ use Maasha::NCBI;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $data_in, $num, $entry, $records, $soft_index,
+my ( $options, $in, $out, $record, $data_in, $num, $entry, $records, $soft_index,
      $fh, @platforms, $plat_table, @samples, $sample, $old_end, $skip, $file );
 
 $options = Maasha::Biopieces::parse_options(
@@ -62,6 +64,8 @@ foreach $file ( @{ $options->{ "data_in" } } )
 
     $soft_index = Maasha::NCBI::soft_index_file( $file );
 
+    # print STDERR Dumper( $soft_index ) if $options->{ "verbose" };
+
     $fh         = Maasha::Filesys::file_read_open( $file );
 
     @platforms  = grep { $_->{ "SECTION" } =~ /PLATFORM/ } @{ $soft_index };
@@ -103,25 +107,22 @@ NUM:
 close $data_in if $data_in;
 close $fh if $fh;
 
+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();
 }