Commit 57d73b5a authored by Ian Longden's avatar Ian Longden
Browse files

check for rna_edit is within the region of interest

parent 3f19b86f
......@@ -252,11 +252,15 @@ sub _rna_edit {
my $slice = shift;
my $seq = shift; #reference to string
my $offset = $slice->start; #substr start at 0 , but seq starts at 1 (so no -1 here)
my $s_start = $slice->start; #substr start at 0 , but seq starts at 1 (so no -1 here)
my $s_end = $s_start+length($$seq);
foreach my $edit (@{$self->{_rna_edits_cache}->{$slice->get_seq_region_id}}){
my ($start, $end, $txt) = split (/\s+/, $edit);
substr($$seq,$start-$offset, ($end-$start)+1, $txt);
# check that RNA edit is not outside the requested region : happens quite often with LRG regions
next if ($end < $s_start);
next if ($s_end < $start);
substr($$seq,$start-$s_start, ($end-$start)+1, $txt);
}
return;
}
......
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