Re-implemented some of the changes from the experimental branch, do not use this commit
Updated merge code.
The following changes have been implemented:
1) The code warns about Havana pseudogenes that have more than one transcript
2) The code tags any Havana genes that have a transcript with attribute gene_cluster.
   In this scenario, any Ensembl genes that have overlapping transcripts are either
   merged or the transcript/gene is thrown out
3) If the Havana xref tag info is not present in the config file then it throws
4) If the Havana gene is a pseudogene a check is now present to see if the Ensembl
   transcript that is being copied in is ccds, if it is then the Ensembl transcript
   takes precedence and the biotype of the gene is updated
5) If the Havana gene is non-coding, but not a pseudogene, and the Ensembl transcript
   being copied is coding, the exon phases are now stripped if the Ensembl transcript
   is not ccds (this is in addition to the translation being removed)
6) If the biotype of the Havana gene is bad, at the moment that's TEC or artifact,
   then skip storing the Havana gene and throw out any overlapping Ensembl genes. In
   both cases a warning is printed showing the gene stable ids of anything affected
Updated merge.pl
Removed an incorrect print and fixed some indentation
Added in the wrapper update
Updated merge.pl
Changed the logic around in the copy method to use unless instead of if(! as it reads
easier this way. Added heavy commenting in the copy method for the different cases as
it's important to be clear about exactly what each one does. Put in a check to see if
the Ens transcript is CCDS when looking at gene clusters. If it is then it's kept
instead of being thrown out and the biotype of the Havana gene is updated the CCDS
transcript biotype if needed.
Update to merge.pl.
Fixed a syntax error in the last commit. Should really perl -c things before committing
Merge branch 'dev/mergecode'