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 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

james-monkeyshines/ensembl-analysis,mn1/ensembl-analysis,Ensembl/ensembl-analysis,mn1/ensembl-analysis,Ensembl/ensembl-analysis,mn1/ensembl-analysis,kiwiroy/ensembl-analysis,james-monkeyshines/ensembl-analysis,james-monkeyshines/ensembl-analysis,kiwiroy/ensembl-analysis,Ensembl/ensembl-analysis