Add Sequence Validation Warnings to jsonwriter.py

[rbaldwin-bugseq]

This PR was a response to this issue:

Handling of X amino acids/masked sequences · Issue #110 · PoonLab/sierra-local

Here's the original input:
K03455_masked.fna.gz

Here's the results of this branch based on that input:
results.json

I tried to match sierra behavior as much as possible

Enhanced Sequence Validation Warnings
File: sierra-local/sierralocal/jsonwriter.py

Drug Resistance Position (DRP) Tracking (lines 123-140)
Added drug_resistance_positions dictionary to track positions where drugClass != 'Other'
Populated from mut_type_pairs.csv during initialization
Used to identify critical positions for drug resistance

Ambiguous Position Warnings at DRPs (lines 490-528)
Detects ambiguous bases (X) or unsequenced positions at drug resistance positions
Issues severity-based warnings:
SEVERE WARNING: More than 5 ambiguous DRPs
WARNING: 2-5 ambiguous DRPs
NOTE: 1 ambiguous DRP
Lists specific positions affected

Unusual Indel Validation (lines 490-528)
Validates only indels (insertions/deletions) as unusual, not all unusual mutations,  to match Stanford Sierra's approach
Issues WARNING with list of unusual indels found
Format: "The {gene} gene has N unusual indel(s): {list}"

Enhanced validate_sequence() Parameters (lines 436-443)
Added mutation_lists: mutation data per gene
Added sequence_name: sequence identifier
Added ambiguous: dictionary of ambiguous positions per gene/sequence
Allows comprehensive validation of mutation quality

Helper Method: is_drug_resistance_position() (lines 666-675)
New method to check if a position is a drug resistance position
Uses the drug_resistance_positions dictionary built during initialization