modified same codon calculation to allow more than 1 allele in the same position from different source

optional extra parameter of the sequence so that if it is passed the sequence is not reloaded for dumping

added section to deal with alleles and transcripts on different strands.  Changed  creating consequenc type using allele strand to creating the consequenceType using the transcript strand.  Changed code so empty object is added to the array rather than none so the number of ConsequenceType Objects matches the number of allele objects

version_check changed to only check when adaptors are instantiated or not at all if special file exists

a bug fix to column allele_string in transcript_variation table. The error is caused by a deletion, such as TTG/- in CTTGTT so the allele_string should be LV/L rather than LV/-

add upstream/downstream flanking 5kb around transcript when consider a variation is involved in the transcript

Use warning() from Bio::EnsEBML::Utils::Exception instead of warn() from Bio::EnsEMBL::Root.
Fix warning message in pop_stack()