fix(advntr): TypeError: cannot convert float NaN to integer during genotype command

[berntpopp]

When running the pipeline subcommand with --extra-modules advntr, a TypeError occurs in the adVNTR HMM alignment step:

2024-12-24 12:28:51,082 - root - ERROR - Error during processing of deletions and insertions: cannot convert float NaN to integer
...
TypeError: unsupported operand type(s) for +=: 'NoneType' and 'str'

This error prevents adVNTR from completing successfully and halts the pipeline.

Steps to Reproduce

1. Run vntyper pipeline --bam /path/to/example.bam --threads 4 --reference-assembly hg19 --keep-intermediates -o out/example_1 --archive-results --extra-modules advntr
2. Observe the TypeError in the output log.

Expected Behavior

• Pipeline should complete adVNTR genotyping without encountering a TypeError.
• Any potential NaN or NoneType values should be handled gracefully or converted properly.

Environment

• advntr==1.3.3
• vntyper==2.0.0-alpha.xx (or current version)
• Python version, OS, conda environment details, etc.

Additional Context

• A potential fix exists in a private branch: enhanced_hmm. Requires thorough testing before merging.

Possible Solutions

• Merge the enhanced_hmm branch changes into the main or stable branch of adVNTR.
• Add checks to handle NaN or type mismatches inside the HMM alignment logic.