use Maasha::Matrix;
use Maasha::Filesys;
use Maasha::UCSC;
+use Maasha::UCSC::Wiggle;
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
$phastcons_file = Maasha::Config::genome_phastcons( $options->{ "genome" } );
$phastcons_index = Maasha::Config::genome_phastcons_index( $options->{ "genome" } );
-$index = Maasha::UCSC::fixedstep_index_retrieve( $phastcons_index );
+$index = Maasha::UCSC::Wiggle::fixedstep_index_retrieve( $phastcons_index );
$fh_phastcons = Maasha::Filesys::file_read_open( $phastcons_file );
while ( $record = Maasha::Biopieces::get_record( $in ) )
{
if ( $record->{ "CHR" } and $record->{ "CHR_BEG" } and $record->{ "CHR_END" } )
{
- $scores = Maasha::UCSC::fixedstep_index_lookup( $index, $fh_phastcons, $record->{ "CHR" },
+ $scores = Maasha::UCSC::Wiggle::fixedstep_index_lookup( $index, $fh_phastcons, $record->{ "CHR" },
$record->{ "CHR_BEG" },
$record->{ "CHR_END" },
$options->{ "flank" } );