From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Mon, 7 Sep 2009 18:33:19 +0000 (+0000)
Subject: sanitized create_bowtie_seq
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=2224c1fb8cbef6483285ba6989a9a09768c15151;p=biopieces.git

sanitized create_bowtie_seq

git-svn-id: http://biopieces.googlecode.com/svn/trunk@658 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/bp_bin/create_bowtie_index b/bp_bin/create_bowtie_index
index b8949ea..fa6b99a 100755
--- a/bp_bin/create_bowtie_index
+++ b/bp_bin/create_bowtie_index
@@ -43,13 +43,14 @@ my ( $default, $formats, $options, $in, $out, $record, $tmp_dir, $file_tmp, $fh_
 $options = Maasha::Biopieces::parse_options(
     [
         { long => 'no_stream',  short => 'x', type => 'flag',   mandatory => 'no',  default => undef, allowed => undef, disallowed => undef },
+        { long => 'directory',  short => 'd', type => 'dir',    mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
         { long => 'index_name', short => 'i', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
     ]   
 );
 
-Maasha::Common::error( qw(directory already exists: "$options->{ 'index_name' }") ) if -d $options->{ 'index_name' };
+Maasha::Common::error( qw(Directory already exists: "$options->{ 'directory' }") ) if -d $options->{ 'directory' };
 
-Maasha::Filesys::dir_create_if_not_exists( $options->{ 'index_name' } );
+Maasha::Filesys::dir_create_if_not_exists( $options->{ 'directory' } );
 
 $in  = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
 $out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
@@ -69,12 +70,10 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
 
 close $fh_tmp;
 
-Maasha::Bowtie::bowtie_index( $file_tmp, $options->{ 'index_name' }, $options->{ 'index_name' }, $options->{ 'verbose' } );
+Maasha::Bowtie::bowtie_index( $file_tmp, $options->{ 'directory' }, $options->{ 'index_name' }, $options->{ 'verbose' } );
 
 unlink $file_tmp;
 
-Maasha::Filesys::dir_remove( $tmp_dir );
-
 Maasha::Biopieces::close_stream( $in );
 Maasha::Biopieces::close_stream( $out );