separate code for PosVarParsimony SAI calculation

[westram]

Motivation:

• needed by SILVA pipeline

Goal:

• code to calculate posvar-SAI shall move into its own library (separated from GUI code and ARB_NTREE)
• functionality needed in pipeline:
  1. load from file
  2. calculate SAI from + sequences
  3. delete

Proposed interface:

1. new function

   GB_ERROR TREE_load_to_db(GBDATA *gb_main, 
                            const char *treefile, 
                            const char *treename);
   

2. new function

   GB_ERROR PVP_calculate(GBDATA *gb_main,
                          const char *ali_name,
                          const char *tree_name,
                          const char *target_SAI_name);
   

3. to delete a from database simply use

   GB_ERROR error = NULL;
   {
     GB_transaction ta(gb_main);
     GBDATA *gb_tree = GBT_find_tree(gb_main, name);
     if (gb_tree) error = GB_delete(gb_tree);
   }
   

Put 1. into ​SL/TREE_READ and 2. into new library.

[westram]

CLI tool added by [16919]:

> bin/arb_calc_pvp --help

arb_calc_pvp -- calculate positional variability SAI
Usage: arb_calc_pvp [switches] <database> <treename> <aliname>

switches:
--savename <dbname>        save database with different name
                           (default is to overwrite input <database>)
--tree-import <treefile>   load tree from <treefile> + store in database as <treename>
                           (default: use tree existing in database)
--tree-delete              delete tree <treename> (before saving database)
--sainame <sai>            use alternate SAI name (default: POS_VAR_BY_PARSIMONY)