From 0b480921aeb83bcaea237880d10f0e4ed59f4c76 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Fri, 27 Aug 2010 16:00:31 +0000
Subject: [PATCH] In check_and_register(): Modify commented out sanity check so
that it's throw() has the correct message (but leave it commented out since
it would stop circular genomes working).
In overlap_size(): Correct documentation.
All from Michael S.
---
modules/Bio/EnsEMBL/Mapper/RangeRegistry.pm | 15 +++++++++------
1 file changed, 9 insertions(+), 6 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Mapper/RangeRegistry.pm b/modules/Bio/EnsEMBL/Mapper/RangeRegistry.pm
index e131c836d3..b53eb490fc 100644
--- a/modules/Bio/EnsEMBL/Mapper/RangeRegistry.pm
+++ b/modules/Bio/EnsEMBL/Mapper/RangeRegistry.pm
@@ -154,14 +154,17 @@ sub check_and_register {
throw("ID, start, end arguments are required");
}
+ # The following was commented out due to Ensembl Genomes requirements
+ # for bacterial genomes.
+ #
## if ( $start > $end ) {
- ## throw("start argument [$start] must be less than end argument [$end]");
+ ## throw( "start argument [$start] must be less than "
+ ## . "(or equal to) end argument [$end]" );
## }
-
+ ##
## if ( $rstart > $rend ) {
- ## throw(
- ## "rend [$rstart] argument must be less than rend [$rend] argument"
- ## );
+ ## throw( "rstart argument [$rstart] must be less than "
+ ## . "(or equal to) rend argument [$rend] argument" );
## }
if ( $rstart > $start ) {
@@ -284,7 +287,7 @@ sub check_and_register {
Arg [1] : string $id
Arg [2] : int $start
- Arg [1] : int $end
+ Arg [3] : int $end
Example : my $overlap_size = $rr->( "chr1", 1, 100_000_000 )
Description: finds out how many bases of the given range are registered
Returntype : int
--
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