fixed rename bug

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

diff --git a/code_perl/Maasha/Biopieces.pm b/code_perl/Maasha/Biopieces.pm
index b910f9af63fe54cb26ce0bcf9181a4a7a0463665..6c38e430698324319052305b5c1c3afcf5fd84dc 100644 (file)
--- a/code_perl/Maasha/Biopieces.pm
+++ b/code_perl/Maasha/Biopieces.pm
@@ -1426,7 +1426,7 @@ sub script_read_fixedstep
 {
     # Martin A. Hansen, Juli 2008.
 
-    # Read fixedStep wiggle format from stream or file.
+    # Read fixedstep wiggle format from stream or file.
 
     my ( $in,        # handle to in stream
          $out,       # handle to out stream
@@ -3105,7 +3105,7 @@ sub script_get_genome_phastcons
     $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 );
 
     if ( defined $options->{ "chr" } and defined $options->{ "beg" } and ( defined $options->{ "end" } or defined $options->{ "len" } ) )
@@ -3117,7 +3117,7 @@ sub script_get_genome_phastcons
             $options->{ "end" } = $options->{ "beg" } + $options->{ "len" } - 1;
         }
 
-        $scores = Maasha::UCSC::phastcons_index_lookup( $index, $fh_phastcons, $options->{ "chr" }, $options->{ "beg" }, $options->{ "end" }, $options->{ "flank" } );
+        $scores = Maasha::UCSC::fixedstep_index_lookup( $index, $fh_phastcons, $options->{ "chr" }, $options->{ "beg" }, $options->{ "end" }, $options->{ "flank" } );
 
         $record->{ "CHR" }       = $options->{ "chr" };
         $record->{ "CHR_BEG" }   = $options->{ "beg" } - $options->{ "flank" };