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
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

mjg17/ensembl,muffato/ensembl,mjg17/ensembl,Ensembl/ensembl,mjg17/ensembl,james-monkeyshines/ensembl,willmclaren/ensembl,willmclaren/ensembl,mjg17/ensembl,Ensembl/ensembl,danstaines/ensembl,danstaines/ensembl,at7/ensembl,at7/ensembl,danstaines/ensembl,muffato/ensembl,Ensembl/ensembl,james-monkeyshines/ensembl,at7/ensembl,Ensembl/ensembl,james-monkeyshines/ensembl,muffato/ensembl,james-monkeyshines/ensembl,at7/ensembl,muffato/ensembl