Reorganise all MSA functionalities in a novel class
The things changed by this merge request:
- create novel MultiSequenceAlignment class
- move all MSA functionalities from pangenome.Classification to pangenome.MultiSequenceAlignment
- remove large parts of redundancy between
pantools msa_of_groups
,pantools msa_of_multiple_groups
andpantools msa_of_regions
, since they only differ in input files - let
pantools consensus_tree
andpantools core_snp_tree
use the novel MSA class (since they also had their own MSA code that was largely copied...) - add novel MSA functionality for aligning sequences based on containing a specific function
- make one MSA function that can be used as:
pantools msa
- update help for integration of all MSA functionalities, can be checked by:
pantools msa -h
Other changes:
- remove build.xml file (belonged to Ant, but we are using Maven now)
- some spelling mistakes
- removed large amounts of pangenome.Classification that are unused