Commit 5e6ae3b5 authored by Philip Lijnzaad's avatar Philip Lijnzaad
Browse files

now uses the `new` (since January 6th ...) convention using local exon coords for start and end

parent 8c942126
......@@ -479,6 +479,23 @@ sub _make_translation {
$translation_end = [$end, $exon->id];
}
### these start/ends are in fpc contig coords; we now have to map it
### back to exon coords (the new convention);
{ my ($start, $exonid) = @$translation_start;
$start -= $transcript->start_exon->start;
$start +=1;
$translation_start = [ $start, $exonid ];
}
# and same for end:
{ my ($end, $exonid) = @$translation_end;
$end -= $transcript->end_exon->start;
$end +=1;
$translation_end = [ $end, $exonid ] ;
}
### $translation_start/end are in fpc coords; have to translate them
### to exon coords, since that's what's expected now
# New translation object
my $translation = Bio::EnsEMBL::Translation->new;
$translation->id($transcript->id);
......
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