From b163367c117597861aa3fd872be8c84dd66d5b74 Mon Sep 17 00:00:00 2001
From: ens-bwalts <bwalts@ebi.ac.uk>
Date: Tue, 19 Nov 2019 16:19:04 +0000
Subject: [PATCH] Fixed Mapper _dump to work again and provide more useful
output
---
modules/Bio/EnsEMBL/Mapper.pm | 30 +++++++++++++++++++++++++++---
1 file changed, 27 insertions(+), 3 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Mapper.pm b/modules/Bio/EnsEMBL/Mapper.pm
index af94c8bcb9..801f932ecd 100644
--- a/modules/Bio/EnsEMBL/Mapper.pm
+++ b/modules/Bio/EnsEMBL/Mapper.pm
@@ -1023,12 +1023,36 @@ sub _dump{
if( !defined $fh ) {
$fh = \*STDERR;
}
- foreach my $id ( keys %{$self->{'_pair_hash_from'}} ) {
- print $fh "From Hash $id\n";
- foreach my $pair ( @{$self->{'_pair_hash_from'}->{uc($id)}} ) {
+
+ my $from = $self->{'from'};
+ my $to = $self->{'to'};
+
+ print $fh "--------------------begin mapper dump--------------------\n";
+ print $fh "dumping from-hash _pair_$from\n";
+ foreach my $id ( keys %{$self->{"_pair_$from"}} ) {
+ print $fh "{_pair_$from}->{" . uc($id) . "}:\n";
+ foreach my $pair ( @{$self->{"_pair_$from"}->{uc($id)}} ) {
print $fh " ",$pair->from->start," ",$pair->from->end,":",$pair->to->start," ",$pair->to->end," ",$pair->to->id,"\n";
}
+ if (defined($self->{"_tree_$from"}->{uc($id)})) {
+ print $fh "{_tree_$from}->{" . uc($id) . "} instantiated\n";
+ } else {
+ print $fh "{_tree_$from}->{" . uc($id) . "} empty\n";
+ }
+ }
+ print $fh "dumping to-hash _pair_$to\n";
+ foreach my $id ( keys %{$self->{"_pair_$to"}} ) {
+ print $fh "{_pair_$to}->{" . uc($id) . "}:\n";
+ foreach my $pair ( @{$self->{"_pair_$to"}->{uc($id)}} ) {
+ print $fh " ",$pair->to->start," ",$pair->to->end,":",$pair->from->start," ",$pair->from->end," ",$pair->from->id,"\n";
+ }
+ if (defined($self->{"_tree_$to"}->{uc($id)})) {
+ print $fh "{_tree_$to}->{" . uc($id) . "} instantiated\n";
+ } else {
+ print $fh "{_tree_$to}->{" . uc($id) . "} empty\n";
+ }
}
+ print $fh "---------------------end mapper dump---------------------\n";
}
--
GitLab