Update EGPairAligner_conf.pm

Moved remove_inconsistencies_after_net ahead of create_filter_duplicates_net_jobs in the workflow. Seems it was unconsistent before with 'remove_inconsistencies_after_net' waiting for 'filter_duplicates_net' and 'create_filter_duplicates_net_jobs' waiting for 'remove_inconsistencies_after_net'!
Update PairAligner_conf.pm

Moved 'remove_inconsistencies_after_net' ahead of 'create_filter_duplicates_net_jobs' in the workflow. Seems it was unconsistent before with 'remove_inconsistencies_after_net' waiting for 'filter_duplicates_net' and 'create_filter_duplicates_net_jobs' waiting for 'remove_inconsistencies_after_net'!
Update EGPairAligner_conf.pm

formatting
updated schema version to 76
Merge pull request #11 from arnaudxk/master

Master
fetch_all_by_column_names in HMMProfile adaptor now returns an arrayref
typo: "hmmer2_home" should be used
No stable ID for homologies
No hash key for PeptideAlignFeature
updated for 76
Merge branch 'master' of https://github.com/Ensembl/ensembl-compara
removed commented code
Added GeneTreeHash file
Merge branch 'master' of https://github.com/Ensembl/ensembl-compara
Up-to-date type constraints in  PeptideAlignFeatureAdaptor
We need to make sure we have up-to-date cache
Merge branch 'master' into feature/hmm_classification

* master:
  Added GeneTreeHash file
  removed commented code
  updated for 76
  fetch_all_by_column_names in HMMProfile adaptor now returns an arrayref
  updated schema version to 76
  Update EGPairAligner_conf.pm
  Update PairAligner_conf.pm
  Update EGPairAligner_conf.pm
fixed GeneTreeHash path
bugfix for the root tag "removed_columns"

The method in Utils can now divide all the coordinates by 3. The bug was
that the runnable was trying to do that on the string, thinking it was an
array
The 3-argument do() method is in DBI, not DBConnection