Running SMAP haplotype-sites using the following options:

Input & output:
    Alignments directory: 00_Data
    Bed file: 96target_AS_Robrecht.bed
    VCF file: bcf.vcf
    Mapping Orientation: ignore
    Output file basename: 05_haplotype-sites

Discrete calls options:
    Discrete call mode: dosage
    Frequency bounds: [10.0, 10.0, 90.0, 90.0]
    Dosage filter: 2
    Locus correctness filter: 0

Graphical output options:
    Plot mode: summary
    Plot type: png

File formatting options:
    Mask frequency: 0
    Undefined_representation: <NA>

Filtering options:
    Remove haplotypes with indels: True
    Include haplotypes with partial alignment: exclude
    Minimum read mapping quality: 30
    Minimum number of haplotypes per locus: 2
    Maximum number of haplotypes per locus: inf
    Minimum read count per locus in each sample: 10
    Maximum read count per locus in each sample: inf
    Minimum haplotype frequency: 2.0

System resources:
    Number of processes: 8

2023-06-12 10:52:22,586 Haplotype - INFO: Loading stack regions and their SMAP and variant positions.
2023-06-12 10:52:22,588 Haplotype - INFO: Removing non-polymorphic stacks.
2023-06-12 10:52:22,588 Haplotype - INFO: Checking the VCF file for a header.
2023-06-12 10:52:22,780 Haplotype - INFO: 10 non-polymorphic stacks were ignored.
2023-06-12 10:52:22,780 Haplotype - INFO: Building haplotypes for 86 stacks of which 86 overlap with min. 1 variant position.
2023-06-12 10:52:22,782 Haplotype - INFO: Found 364 bam files.
2023-06-12 10:52:22,782 Haplotype - INFO: Started haplotyping 364 bam files.
2023-06-12 10:52:22,826 Haplotype - INFO: Started joining columns for stack counts.
2023-06-12 10:53:20,120 Haplotype - INFO: Haplotyping done.
2023-06-12 10:53:20,186 Haplotype - INFO: Removing haplotypes with indels.
2023-06-12 10:53:20,232 Haplotype - INFO: Removing haplotypes that cover only parts of the regions.
2023-06-12 10:53:25,716 Haplotype - INFO: Filtering to remove haplotypes with low read frequency.
2023-06-12 10:53:26,924 Haplotype - INFO: Calculating discrete calls.
2023-06-12 10:53:27,899 Haplotype - INFO: Filtering dosage table to remove loci with unexpected total dosage calls.
2023-06-12 10:53:34,864 Haplotype - INFO: Finished