Index

Symbols

--version grid command line option

-v grid command line option

_

_compute_imp() (in module grid.utils.hi_inference) _get_nested() (in module grid.config) _is_enabled() (in module grid.config) _load_ibd_neighbors() (in module grid.utils.hi_inference)

_load_ibs_neighbors() (in module grid.utils.hi_inference) _read_dip_cn_file() (in module grid.utils.hi_inference) _run_phasing() (in module grid.utils.hi_inference) _segment_distance() (in module grid.utils.hi_inference)

B

build_depth_matrix() (in module grid.utils.normalize_mosdepth)

build_matrix_from_regions() (in module grid.utils.normalize_mosdepth) build_mosdepth_command() (in module grid.utils.mosdepth)

C

check_index() (in module grid.utils.utils) check_mosdepth_available() (in module grid.utils.mosdepth) compute_diploid_genotypes() (in module grid.utils.compute_dipcn) compute_mosdepth() (in module grid.utils.mosdepth) compute_population_mean_depths() (in module grid.utils.normalize_mosdepth) compute_region_coverage() (in module grid.utils.mosdepth)

CONFIG grid-wgs command line option count_reads() (in module grid.utils.count_reads) count_reads_in_region() (in module grid.utils.count_reads) create_index() (in module grid.utils.utils) create_index_for_file() (in module grid.utils.utils) create_region_string() (in module grid.utils.utils)

E

ensure_crai() (in module grid.utils.ensure_crai)

error_check_config() (in module grid.config)

F

filter_empty_samples() (in module grid.utils.normalize_mosdepth) filter_regions_by_variance() (in module grid.utils.find_neighbors) find_bed_gz_for_individual() (in module grid.utils.normalize_mosdepth)

find_file() (in module grid.utils.utils) find_neighbors() (in module grid.utils.find_neighbors) find_neighbors_sklearn() (in module grid.utils.find_neighbors)

G

get_flags() (in module grid.utils.utils) get_samples() (in module grid.utils.utils) grid command line option --version -v grid-wgs command line option CONFIG grid.cli module grid.config module grid.pipeline module grid.utils.compute_dipcn module

grid.utils.count_reads module grid.utils.ensure_crai module grid.utils.find_neighbors module grid.utils.hi_inference module grid.utils.mosdepth module grid.utils.normalize_mosdepth module grid.utils.utils module

H

has_index() (in module grid.utils.utils)

hi_inference() (in module grid.utils.hi_inference)

L

load_neighbors() (in module grid.utils.compute_dipcn)

load_repeat_mask() (in module grid.utils.normalize_mosdepth) log() (in module grid.utils.utils)

M

main() (in module grid.cli) map_mosdepth_files_to_samples() (in module grid.utils.normalize_mosdepth) module grid.cli grid.config grid.pipeline grid.utils.compute_dipcn grid.utils.count_reads grid.utils.ensure_crai grid.utils.find_neighbors grid.utils.hi_inference grid.utils.mosdepth grid.utils.normalize_mosdepth grid.utils.utils

N

norm_chrom() (in module grid.utils.normalize_mosdepth)

normalize_matrix() (in module grid.utils.normalize_mosdepth) normalize_mosdepth() (in module grid.utils.normalize_mosdepth)

O

open_maybe_gz() (in module grid.utils.utils)

P

print_banner() (in module grid.cli) print_version_and_exit() (in module grid.cli)

process_one_individual() (in module grid.utils.normalize_mosdepth) process_single_cram() (in module grid.utils.count_reads) progress_bar() (in module grid.utils.utils)

R

read_normalized_data() (in module grid.utils.find_neighbors) remove_intermediate_files() (in module grid.utils.mosdepth)

run_mosdepth_single_cram() (in module grid.utils.mosdepth) run_wgs_pipeline() (in module grid.pipeline)

S

save_neighbors() (in module grid.utils.find_neighbors)

select_high_variance_regions() (in module grid.utils.normalize_mosdepth) setup_output_file() (in module grid.utils.utils)

V

validate_steps() (in module grid.config)

validate_top_level() (in module grid.config)

W

wait_for_mosdepth_output() (in module grid.utils.mosdepth) write_coverage_result() (in module grid.utils.mosdepth)

write_normalized_output() (in module grid.utils.normalize_mosdepth) write_read_results() (in module grid.utils.count_reads)