New parameters to set the location of the ortheus executable, the method_link_type and species_set_name of the alignment.
Also, parameters like the flank size and max. alignment length are set to their default values if not set by the user/pipeline.

There is a new parameter called "example" that sets most of the values such that it is easier for anyone to test to the code
with a toy region.
Changes in the modules to infer the AncestralAlleles for 1-bp indels

New parameters to set the location of the ortheus executable, the method_link_type and species_set_name of the alignment.

Also, parameters like the flank size and max. alignment length are set to their default values if not set by the user/pipeline.

There is a new parameter called "example" that sets most of the values such that it is easier for anyone to test to the code
with a toy region.

Slightly modified the output in the indel_X_XXXXXX_XXXXX file to report the final call.
Fix the warning message in case of missing dnafrag
Merge pull request #2 from jherrero/master

Small changes in the modules for the AncestralAlleles for 1-bp indels
Cosmetic changes suggested by podchecker
Merge remote-tracking branch 'github/release/75'

* github/release/75:
  Fix the warning message in case of missing dnafrag
Merge branch 'master' into feature/hmm_classification

* master:
  Cosmetic changes suggested by podchecker
  Fix the warning message in case of missing dnafrag
  New parameters to set the location of the ortheus executable, the method_link_type and species_set_name of the alignment. Also, parameters like the flank size and max. alignment length are set to their default values if not set by the user/pipeline.

Conflicts:
	modules/Bio/EnsEMBL/Compara/RunnableDB/ProteinTrees/MultiHMMLoadModels.pm
	modules/Bio/EnsEMBL/Compara/RunnableDB/ProteinTrees/PantherLoadModels.pm