tada

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

diff --git a/code_perl/Maasha/Biopieces.pm b/code_perl/Maasha/Biopieces.pm
index 820005bb639db752ce0af7dd02566848d49c2884..edaccbb6b4e988a0f3fc08d91ee1d6b37595c440 100644 (file)
--- a/code_perl/Maasha/Biopieces.pm
+++ b/code_perl/Maasha/Biopieces.pm
@@ -946,7 +946,7 @@ sub get_options
             group|g=s
             priority|p=f
             use_score|u
-            visibility|v=s
+            visibility|V=s
             color|c=s
             chunk_size|C=s
         );
@@ -955,7 +955,7 @@ sub get_options
     push @options, qw(
         stream_in|I=s
         stream_out|O=s
-        verbose
+        verbose|v
         help|?
     );
 
@@ -4477,14 +4477,17 @@ sub script_plot_phastcons_profiles
     $phastcons_file  = Maasha::Config::genome_phastcons( $options->{ "genome" } );
     $phastcons_index = Maasha::Config::genome_phastcons_index( $options->{ "genome" } );
 
-    $index           = Maasha::UCSC::phastcons_index_retrieve( $phastcons_index );
+    $index           = Maasha::UCSC::fixedstep_index_retrieve( $phastcons_index );
     $fh_phastcons    = Maasha::Common::read_open( $phastcons_file );
 
     while ( $record = get_record( $in ) ) 
     {
         if ( $record->{ "CHR" } and $record->{ "CHR_BEG" } and $record->{ "CHR_END" } )
         {
-            $scores = Maasha::UCSC::phastcons_index_lookup( $index, $fh_phastcons, $record->{ "CHR" }, $record->{ "CHR_BEG" }, $record->{ "CHR_END" }, $options->{ "flank" } );
+            $scores = Maasha::UCSC::fixedstep_index_lookup( $index, $fh_phastcons, $record->{ "CHR" },
+                                                                                   $record->{ "CHR_BEG" },
+                                                                                   $record->{ "CHR_END" },
+                                                                                   $options->{ "flank" } );
 
             push @{ $AoA }, [ @{ $scores } ];
         }