From 82cc2d402135a13aa4ae1cc7f9ba2c535bef8e10 Mon Sep 17 00:00:00 2001
From: Patrick Meidl <pm2@sanger.ac.uk>
Date: Thu, 17 Apr 2008 13:35:18 +0000
Subject: [PATCH] fixed bug in load_and_merge() when using
--cache_method=build_cache_all
---
modules/Bio/EnsEMBL/IdMapping/Cache.pm | 25 +++++++++++++++++++++++--
1 file changed, 23 insertions(+), 2 deletions(-)
diff --git a/modules/Bio/EnsEMBL/IdMapping/Cache.pm b/modules/Bio/EnsEMBL/IdMapping/Cache.pm
index 1b41018c44..ebd6a8d72f 100644
--- a/modules/Bio/EnsEMBL/IdMapping/Cache.pm
+++ b/modules/Bio/EnsEMBL/IdMapping/Cache.pm
@@ -155,6 +155,9 @@ sub build_cache_by_slice {
# write cache to file, then flush cache to reclaim memory
my $size = $self->write_all_to_file($type);
+ # set cache method (required for loading cache later)
+ $self->cache_method('BY_SEQ_REGION');
+
return $num_genes, $size;
}
@@ -199,6 +202,9 @@ sub build_cache_all {
# write cache to file, then flush cache to reclaim memory
my $size = $self->write_all_to_file($type);
+ # set cache method (required for loading cache later)
+ $self->cache_method('ALL');
+
return $num_genes, $size;
}
@@ -1052,8 +1058,16 @@ sub read_and_merge {
throw("Db type must be 'source' or 'target'.");
}
- foreach my $slice_name (@{ $self->slice_names($dbtype) }) {
- $self->read_from_file("$dbtype.$slice_name");
+ # read cache from single or multiple files, depending on caching strategy
+ my $cache_method = $self->cache_method;
+ if ($cache_method eq 'ALL') {
+ $self->read_from_file("$dbtype.ALL");
+ } elsif ($cache_method eq 'BY_SEQ_REGION') {
+ foreach my $slice_name (@{ $self->slice_names($dbtype) }) {
+ $self->read_from_file("$dbtype.$slice_name");
+ }
+ } else {
+ throw("Unknown cache method: $cache_method.");
}
$self->merge($dbtype);
@@ -1196,6 +1210,13 @@ sub conf {
}
+sub cache_method {
+ my $self = shift;
+ $self->{'instance'}->{'cache_method'} = shift if (@_);
+ return $self->{'instance'}->{'cache_method'};
+}
+
+
sub highest_common_cs {
my $self = shift;
$self->{'instance'}->{'hccs'} = shift if (@_);
--
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