refactoring of assemble_pairs

[biopieces.git] / bp_bin / calc_fixedstep

diff --git a/bp_bin/calc_fixedstep b/bp_bin/calc_fixedstep
index 9c14f2ca49ed2ca2ae0bed582948926fee64b46e..e98b63a9c8828337f093310573e59a08e7164c86 100755 (executable)
--- a/bp_bin/calc_fixedstep
+++ b/bp_bin/calc_fixedstep
@@ -1,6 +1,6 @@
-#!/usr/bin/env perl -w
+#!/usr/bin/env perl
 
-# Copyright (C) 2007-2009 Martin A. Hansen.
+# Copyright (C) 2007-2010 Martin A. Hansen.
 
 # This program is free software; you can redistribute it and/or
 # modify it under the terms of the GNU General Public License
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Filesys;
@@ -36,12 +37,13 @@ use Maasha::UCSC::Wiggle;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $tmp_dir, $bed_file, $fh_in, $fh_out,
+my ( $options, $in, $out, $record, $tmp_dir, $bed_file, $fh_in, $fh_out,
      $file_hash, $chr, $bed_entry, $fixedstep_file, $fixedstep_entry );
 
 $options = Maasha::Biopieces::parse_options(
     [
         { long => 'check', short => 'C', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+        { long => 'log10', short => 'l', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
     ]   
 );
 
@@ -72,7 +74,7 @@ foreach $chr ( sort keys %{ $file_hash } )
 {
     $bed_file       = $file_hash->{ $chr };
 
-    $fixedstep_file = Maasha::UCSC::Wiggle::fixedstep_calc( $bed_file, $chr, $options->{ 'use_score' }, $options->{ 'use_log10' } );        
+    $fixedstep_file = Maasha::UCSC::Wiggle::fixedstep_calc( $bed_file, $chr, $options->{ 'log10' } );        
 
     #$fixedstep_file = "$bed_file.fixedstep";
     
@@ -93,7 +95,8 @@ foreach $chr ( sort keys %{ $file_hash } )
     unlink $fixedstep_file;
 }
 
-Maasha::Filesys::dir_remove( $tmp_dir );
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
 
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
@@ -101,19 +104,13 @@ 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();
 }