refactoring of assemble_pairs

[biopieces.git] / bp_bin / calc_fixedstep

diff --git a/bp_bin/calc_fixedstep b/bp_bin/calc_fixedstep
index 27cae9f22fb64ca3a247800a5e8f26316d9d3f52..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;
@@ -42,6 +43,7 @@ my ( $options, $in, $out, $record, $tmp_dir, $bed_file, $fh_in, $fh_out,
 $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";
     
@@ -93,8 +95,6 @@ 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 );