fixes and stuff

[biopieces.git] / code_perl / Maasha / Biopieces.pm

diff --git a/code_perl/Maasha/Biopieces.pm b/code_perl/Maasha/Biopieces.pm
index 09218a67cdfcfd5acc708585440071affb4ea6e6..867f71b011aaf90326ed38ace14927007623d933 100644 (file)
--- a/code_perl/Maasha/Biopieces.pm
+++ b/code_perl/Maasha/Biopieces.pm
@@ -289,7 +289,12 @@ sub parse_options
 {
     # Martin A. Hansen, May 2009
 
-    # 
+    # Parses and checks options for Biopieces.
+
+    # First the argument list is checked for duplicates and then
+    # options are parsed from ARGV after which it is checked if
+    # the Biopieces usage information should be printed. Finally,
+    # all options from ARGV are checked according to the argument list.
 
     my ( $arg_list,   # data structure with argument description
        ) = @_;
@@ -409,7 +414,7 @@ sub check_print_usage
                
                     if ( exists $options->{ 'help' } ) {
                         `print_wiki --data_in=$wiki --help`;
-                    } elsif ( $script =~ /^(list_biopieces|list_genomes)$/ ) {
+                    } elsif ( $script =~ /^(list_biopieces|list_genomes|biostat)$/ ) {
                         return;
                     } else {
                         `print_wiki --data_in=$wiki`;
@@ -805,38 +810,6 @@ sub clean_tmp
 }
 
 
-sub run_time
-{
-    # Martin A. Hansen, May 2009.
-
-    # Returns a precision timestamp for calculating
-    # run time.
-
-    return Maasha::Common::get_time_hires();
-}
-
-
-sub run_time_print
-{
-    # Martin A. Hansen, May 2009
-
-    # Print the run time to STDERR for the current script if
-    # the verbose switch is set in the option hash.
-
-    my ( $t0,       # run time begin
-         $t1,       # run time end
-         $options,  # options hash
-       ) = @_;
-
-    # Returns nothing
-
-    my $script = Maasha::Common::get_scriptname();
-
-    print STDERR "Program: $script" . ( " " x ( 25 - length( $script ) ) ) . sprintf( "Run time: %.4f\n", ( $t1 - $t0 ) ) if $options->{ 'verbose' };
-
-}
-
-
 sub get_tmpdir
 {
     # Martin A. Hansen, April 2008.