fixed minor bugs

git-svn-id: http://biopieces.googlecode.com/svn/trunk@513 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/get_genome_seq b/bp_bin/get_genome_seq
index b5ea5a70d73ed4c661693674d4ff713d383e5913..737469d4476aef7e0df6a1a13182d21815785362 100755 (executable)
--- a/bp_bin/get_genome_seq
+++ b/bp_bin/get_genome_seq
@@ -68,7 +68,7 @@ if ( $options->{ "genome" } )
 
     map { $lookup_hash{ $_->[ 0 ] } = [ $_->[ 1 ], $_->[ 2 ] ] } @{ $index };
 
-    if ( exists $lookup_hash{ $options->{ "chr" } } and defined $options->{ "beg" } and ( defined $options->{ "end" } or defined $options->{ "len" } ) )
+    if ( defined $options->{ "chr" } and exists $lookup_hash{ $options->{ "chr" } } and defined $options->{ "beg" } and ( defined $options->{ "end" } or defined $options->{ "len" } ) )
     {
         ( $index_beg, $index_len ) = @{ $lookup_hash{ $options->{ "chr" } } };
 

diff --git a/code_perl/Maasha/Biopieces.pm b/code_perl/Maasha/Biopieces.pm
index 44b589b9c0d2cfe6f0d387a69b0fd0e6636f8dc9..09218a67cdfcfd5acc708585440071affb4ea6e6 100644 (file)
--- a/code_perl/Maasha/Biopieces.pm
+++ b/code_perl/Maasha/Biopieces.pm
@@ -302,10 +302,10 @@ sub parse_options
 
     push @{ $arg_list }, (
     
-        { long => 'help',       short => '?', type => 'flag',  mandatory => 'no',  default => undef, allowed => undef, disallowed => undef },
-        { long => 'stream_in',  short => 'I', type => 'file!', mandatory => 'no',  default => undef, allowed => undef, disallowed => undef },
-        { long => 'stream_out', short => 'O', type => 'file',  mandatory => 'no',  default => undef, allowed => undef, disallowed => undef },
-        { long => 'verbose',    short => 'v', type => 'flag',  mandatory => 'no',  default => undef, allowed => undef, disallowed => undef },
+        { long => 'help',       short => '?', type => 'flag',  mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+        { long => 'stream_in',  short => 'I', type => 'file!', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+        { long => 'stream_out', short => 'O', type => 'file',  mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+        { long => 'verbose',    short => 'v', type => 'flag',  mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
     );
 
     check_duplicates_args( $arg_list );