Enhance cooccurring_mutations.csv to include all haplotypes per mutation

[LaraFuhrmann]

Description:

Currently, the cooccurring_mutations.csv file lists one row per mutation. However, when a mutation occurs in multiple haplotypes, only one haplotype is listed in the haplotype column. This limits the information available and may lead to incomplete analysis.

Proposed Enhancement:

We suggest modifying the output to include one row per mutation occurrence in each haplotype. This means:

• If a mutation occurs in multiple haplotypes, there should be a separate row for each of these haplotypes.
• Each row will contain the mutation information along with its corresponding haplotype.

[LaraFuhrmann]

I have tested the fix on tests/data_1 with the command viloca run -a 0.1 -w 201 --mode shorah -x 100000 -p 0.9 -c 0 -r HXB2:2469-3713 -R 42 -f test_ref.fasta -b test_aln.cram --out_format csv "$@"

The fix passes the tests and the cooccurring_mutations.csv file does as intended.
See line 9 and 19 are the same mutation occurring in two different haplotypes.

9,w-HXB2-2268-2468.reads.fas,hap_0-2268-2468,HXB2,2268,2468,39,2432,T,G,0.46194355049812913,1.0
10,w-HXB2-2268-2468.reads.fas,hap_0-2268-2468,HXB2,2268,2468,39,2439,C,G,0.46194355049812913,1.0
11,w-HXB2-2268-2468.reads.fas,hap_0-2268-2468,HXB2,2268,2468,39,2440,T,A,0.46194355049812913,1.0
12,w-HXB2-2268-2468.reads.fas,hap_1-2268-2468,HXB2,2268,2468,39,2453,T,C,0.5380564495018709,1.0
13,w-HXB2-2268-2468.reads.fas,hap_0-2268-2468,HXB2,2268,2468,39,2467,T,A,0.46194355049812913,1.0
14,w-HXB2-2335-2535.reads.fas,hap_1-2335-2535,HXB2,2335,2535,87,2357,A,C,0.5184725950715671,1.0
15,w-HXB2-2335-2535.reads.fas,hap_1-2335-2535,HXB2,2335,2535,87,2361,A,G,0.5184725950715671,1.0
16,w-HXB2-2335-2535.reads.fas,hap_0-2335-2535,HXB2,2335,2535,87,2362,G,A,1.0,1.0
17,w-HXB2-2335-2535.reads.fas,hap_1-2335-2535,HXB2,2335,2535,87,2363,T,G,0.5184725950715671,1.0
18,w-HXB2-2335-2535.reads.fas,hap_1-2335-2535,HXB2,2335,2535,87,2372,A,G,0.5184725950715671,1.0
19,w-HXB2-2335-2535.reads.fas,hap_1-2335-2535,HXB2,2335,2535,87,2432,T,G,0.5184725950715671,1.0
20,w-HXB2-2335-2535.reads.fas,hap_1-2335-2535,HXB2,2335,2535,87,2439,C,G,0.5184725950715671,1.0

[LaraFuhrmann]

• Updated the behaviour such that the posterior threshold (-p) is not applied for mutation filtering in cooccurring_mutations.csv.
• Updated README accordingly

Tested it again on tests/data_1 with the command viloca run -a 0.1 -w 201 --mode shorah -x 100000 -p 0.9 -c 0 -r HXB2:2469-3713 -R 42 -f test_ref.fasta -b test_aln.cram --out_format csv "$@".