Commit 7cb1a222 authored by Magali Ruffier's avatar Magali Ruffier
Browse files

replaced reg variable with registry for consistency

if we use first_registry and last_registry throughout the module, we can probably afford to use registry rather than reg for the simpler cases
parent 16d931b9
......@@ -1509,7 +1509,7 @@ sub register_all_chained {
}
my ( $mid_cs_id, $start_cs_id, $reg, $mapper );
my ( $mid_cs_id, $start_cs_id, $registry, $mapper );
if ( !defined $mid_cs ) {
$mid_cs_id = $last_cs->dbID();
$start_cs_id = $first_cs->dbID();
......@@ -1520,7 +1520,7 @@ sub register_all_chained {
$mapper = $start_mid_mapper;
}
$reg = $casm_mapper->first_registry();
$registry = $casm_mapper->first_registry();
while($sth->fetch()) {
$mapper->add_map_coordinates
......@@ -1530,7 +1530,7 @@ sub register_all_chained {
);
push( @ranges, [$start_seq_region_id, $start_start, $start_end ] );
$reg->check_and_register( $start_seq_region_id, 1, $start_length );
$registry->check_and_register( $start_seq_region_id, 1, $start_length );
if( ! defined $mid_cs ) {
$casm_mapper->last_registry()->check_and_register
( $mid_seq_region_id, $mid_start, $mid_end );
......@@ -1599,7 +1599,7 @@ sub register_all_chained {
}
my $end_cs_id = $last_cs->dbID();
$reg = $casm_mapper->last_registry();
$registry = $casm_mapper->last_registry();
while($sth->fetch()) {
$end_mid_mapper->add_map_coordinates
......@@ -1608,7 +1608,7 @@ sub register_all_chained {
$mid_seq_region_id, $mid_start, $mid_end
);
$reg->check_and_register( $end_seq_region_id, 1, $end_length );
$registry->check_and_register( $end_seq_region_id, 1, $end_length );
my $arr = [ $end_seq_region_id, $end_seq_region,
$end_cs_id, $end_length ];
......
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