BAM-native crossover detection tool that replaces SiMoRec pipeline
rules 08-12 (Extract_genotype, Filter_genotype, Detect_recombinants,
Obtain_co_features) with a single indexed BAM sweep using htslib.

Key features:
- SNP/INS/DEL genotyping via CIGAR walking (no MD tag parsing)
- FNV-1a hash table for molecule tracking (LR BX+MI or HiFi QNAME)
- Optional sliding-window smoothing of allele sequences
- BGZF-compressed primary output + plain-TSV auxiliary output
- Eliminates rule-13 BAM re-access via aux file
- CLI: --bam --markers --output --aux-output --mode --min_marker
        --max_marker --smoothing_window --enable_smoothing
        --min_base_qual (default 32) --threads -h