API Reference

The public interface is the wisp command line tool, but these modules are useful when reading or extending the implementation.

Configuration

class wisp_mask.config.AlignmentRunConfig(samples_path: 'Path', min_dp: 'int | None', out_dir: 'Path', work_dir: 'Path | None' = None, threads: 'int' = 1, jobs: 'int' = 1, mask_bed: 'Path | None' = None, variants_vcf: 'Path | None' = None, min_mapq: 'int | None' = None, max_dp: 'int | None' = None, exclude_flag: 'int | None' = None, include_flag: 'int | None' = None, reference: 'Path | None' = None, fast_mode: 'bool' = False, keep_work: 'bool' = False, force: 'bool' = False, dry_run: 'bool' = False, output_prefix: 'str' = 'wisp')

class wisp_mask.config.VcfRunConfig(all_sites_vcf: 'Path', popfile_path: 'Path', min_dp: 'int', out_dir: 'Path', max_dp: 'int | None' = None, work_dir: 'Path | None' = None, mask_bed: 'Path | None' = None, keep_work: 'bool' = False, force: 'bool' = False, dry_run: 'bool' = False, output_prefix: 'str' = 'wisp', snps_only: 'bool' = False)

Workflow

Samples

wisp_mask.samples.read_popfile(path: Path) → list[Sample]

Read a sample/population TSV with an optional header.

wisp_mask.samples.read_samples(path: Path) → list[Sample]

Read a sample metadata TSV with an optional header.

Output summaries