split update_index_and_logfile.py into 3 scripts, and use Dask

[miseminger]

new scripts are:

• gvf2indexandlog.py: takes one GVF, creates two TSVs: one index, one logfile.
• merge_indices.py: reads all index files from gvf2indexandlog.py, as well as an optional original mutation index, and merges them into a new index using Dask.
• merge_logfiles.py: reads all log files from gvf2indexandlog.py, as well as a log header file, and an optional original mutation index, and merges them into a new log using Dask. It also prints out the number of mutations in the log that have 5 or more corresponding lineages.

the old script, update_index_and_logfile.py, is obsolete after the addition of these three scripts, and can be deleted.

also important to note: the mutation index columns have changed since we last made an index. The new columns are: ['pos', 'mutation', 'hgvs_aa_mutation', 'hgvs_nt_mutation', 'gene', 'protein_name', 'alias', 'hgvs_alias', 'alias_protein', 'Pokay_annotation', 'lineages']

[miseminger]

@miseminger tested with Dask version 2021.10.0. Will update to the current version and check that it still works.

[miseminger]

Please replace the minimal use of pandas with dask in bin/merge_indices.py and bin/merge_logfiles.py scripts and test it on the latest dask version 2023.10.1-py11-ol9_cv1

Latest Dask version (2024.2.1) depends on Pandas 2.2.1; can we update Pandas in environment.yml?