fix: accumulate counts when combining mutations

[gp201]

This pull request updates the mutation chaining logic in the check_mutation_chain function and adds a new unit test to verify its correctness. The main improvements are in how mutations are combined.

Mutation chaining logic update:

• Modified check_mutation_chain in convert_paths2barcodes.py to increment the count of an existing mutation when combining mutations, rather than setting it to 1. This ensures that mutation counts are accurately preserved during chaining.

Testing enhancements:

• Added a new unit test test_check_mutation_chain in test_barcoding.py to verify that mutation chaining produces the expected barcode output when combining mutations.

Example:

A225G > G225T > T225C > C225A > A225T > T225C

• Bug: The code collapses A225G > G225T to A225T. Since A225T is already present in the mutations path instead of incrementing the count of seeing the mutation to 2 it sets to 1.

• Fix: The code has now been patched to increment the count.

lineage_path.txt