Index

Symbols

--bed-file grid-extract-reference command line option --bucket-path grid-gcloud-copy command line option --by grid-mosdepth command line option --chrom grid-count-reads command line option grid-lpa-realign command line option grid-mosdepth command line option grid-normalize-mosdepth command line option grid-subset command line option --config grid-count-reads command line option --count-file grid-compute-dipcn command line option --cram grid-crai command line option grid-subset command line option --cram-dir grid-count-reads command line option grid-gcloud-copy command line option grid-lpa-realign command line option grid-mosdepth command line option --end grid-count-reads command line option grid-lpa-realign command line option grid-mosdepth command line option grid-normalize-mosdepth command line option grid-subset command line option --exon1a grid-estimate-kiv command line option --exon1b grid-estimate-kiv command line option --fast grid-mosdepth command line option --format grid-estimate-kiv command line option --genome-build grid-lpa-realign command line option --input-file grid-find-neighbors command line option --lpa-ref-fasta grid-lpa-realign command line option --max-depth grid-normalize-mosdepth command line option --min-depth grid-normalize-mosdepth command line option --mosdepth-dir grid-normalize-mosdepth command line option --n-neighbors grid-compute-dipcn command line option grid-find-neighbors command line option --neighbor-file grid-compute-dipcn command line option --no-fast grid-mosdepth command line option --output grid-estimate-kiv command line option grid-subset command line option --output-dir grid-extract-reference command line option --output-file grid-count-reads command line option grid-find-neighbors command line option grid-lpa-realign command line option grid-mosdepth command line option grid-normalize-mosdepth command line option --output-prefix grid-compute-dipcn command line option grid-extract-reference command line option --positions-file grid-lpa-realign command line option --ref-fasta grid-count-reads command line option grid-lpa-realign command line option grid-mosdepth command line option --reference grid-crai command line option grid-subset command line option --reference-fa grid-extract-reference command line option --region grid-subset command line option --region-name grid-mosdepth command line option --repeat-mask grid-normalize-mosdepth command line option --sigma2-max grid-find-neighbors command line option --start grid-count-reads command line option grid-lpa-realign command line option grid-mosdepth command line option grid-normalize-mosdepth command line option grid-subset command line option

--threads grid-count-reads command line option grid-lpa-realign command line option grid-mosdepth command line option grid-normalize-mosdepth command line option --top-frac grid-normalize-mosdepth command line option --version grid command line option --work-dir grid-mosdepth command line option --zmax grid-find-neighbors command line option -a grid-estimate-kiv command line option -b grid-estimate-kiv command line option grid-extract-reference command line option grid-gcloud-copy command line option -C grid-count-reads command line option grid-gcloud-copy command line option grid-lpa-realign command line option grid-mosdepth command line option grid-subset command line option -c grid-compute-dipcn command line option grid-count-reads command line option grid-crai command line option grid-lpa-realign command line option grid-mosdepth command line option grid-normalize-mosdepth command line option grid-subset command line option -e grid-count-reads command line option grid-lpa-realign command line option grid-mosdepth command line option grid-normalize-mosdepth command line option grid-subset command line option -f grid-estimate-kiv command line option grid-extract-reference command line option grid-lpa-realign command line option -g grid-lpa-realign command line option -i grid-find-neighbors command line option -M grid-normalize-mosdepth command line option -N grid-compute-dipcn command line option -n grid-compute-dipcn command line option grid-find-neighbors command line option grid-mosdepth command line option -o grid-compute-dipcn command line option grid-count-reads command line option grid-estimate-kiv command line option grid-extract-reference command line option grid-find-neighbors command line option grid-lpa-realign command line option grid-mosdepth command line option grid-normalize-mosdepth command line option grid-subset command line option -P grid-lpa-realign command line option -R grid-subset command line option -r grid-count-reads command line option grid-crai command line option grid-extract-reference command line option grid-lpa-realign command line option grid-mosdepth command line option grid-normalize-mosdepth command line option grid-subset command line option -s grid-count-reads command line option grid-lpa-realign command line option grid-mosdepth command line option grid-normalize-mosdepth command line option grid-subset command line option -t grid-count-reads command line option grid-lpa-realign command line option grid-mosdepth command line option grid-normalize-mosdepth command line option -v grid command line option -w grid-mosdepth command line option -z grid-find-neighbors command line option

_

_process_one_individual() (in module grid.utils.normalize_mosdepth_dir)

B

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

build_matrix_from_regions() (in module grid.utils.normalize_mosdepth_dir) build_mosdepth_command() (in module grid.utils.mosdepth_dir)

C

check_mosdepth_available() (in module grid.utils.mosdepth_dir) classify_read_pairs() (in module grid.utils.align_lpa_dir) classify_variant_from_scores() (in module grid.utils.align_lpa_dir) compute_alignment_scores() (in module grid.utils.align_lpa_dir) compute_dipcn_pipeline() (in module grid.utils.compute_dipcn) compute_diploid_cn_for_exon() (in module grid.utils.compute_dipcn_dir)

compute_kiv2_estimates() (in module grid.utils.estimate_kiv_dir) compute_kiv_estimates() (in module grid.utils.estimate_kiv) compute_region_coverage() (in module grid.utils.mosdepth_dir) compute_summary_stats() (in module grid.utils.estimate_kiv_dir) count_reads() (in module grid.utils.count_reads) count_reads_in_region() (in module grid.utils.count_reads_dir) create_region_string() (in module grid.utils.helper_dir)

E

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

extract_reference() (in module grid.utils.extract_reference) extract_regions() (in module grid.utils.normalize_mosdepth_dir)

F

filter_regions_by_variance() (in module grid.utils.find_neighbors_dir) find_cram_files() (in module grid.utils.align_lpa_dir) (in module grid.utils.helper_dir)

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

G

get_exon_count() (in module grid.utils.compute_dipcn_dir) get_individuals() (in module grid.utils.normalize_mosdepth_dir) grid module grid command line option --version -v grid-compute-dipcn command line option --count-file --n-neighbors --neighbor-file --output-prefix -c -n -N -o grid-count-reads command line option --chrom --config --cram-dir --end --output-file --ref-fasta --start --threads -C -c -e -o -r -s -t grid-crai command line option --cram --reference -c -r grid-estimate-kiv command line option --exon1a --exon1b --format --output -a -b -f -o grid-extract-reference command line option --bed-file --output-dir --output-prefix --reference-fa -b -f -o -r grid-find-neighbors command line option --input-file --n-neighbors --output-file --sigma2-max --zmax -i -n -o -z grid-gcloud-copy command line option --bucket-path --cram-dir -b -C grid-lpa-realign command line option --chrom --cram-dir --end --genome-build --lpa-ref-fasta --output-file --positions-file --ref-fasta --start --threads -C -c -e -f -g -o -P -r -s -t grid-mosdepth command line option --by --chrom --cram-dir --end --fast --no-fast --output-file --ref-fasta --region-name --start --threads --work-dir -C -c -e -n -o -r -s -t -w

grid-normalize-mosdepth command line option --chrom --end --max-depth --min-depth --mosdepth-dir --output-file --repeat-mask --start --threads --top-frac -c -e -M -o -r -s -t grid-subset command line option --chrom --cram --end --output --reference --region --start -c -C -e -o -r -R -s grid.cli module grid.config module grid.pipeline module grid.utils module grid.utils.align_lpa module grid.utils.align_lpa_dir module grid.utils.compute_dipcn module grid.utils.compute_dipcn_dir module grid.utils.count_reads module grid.utils.count_reads_dir module grid.utils.ensure_crai module grid.utils.estimate_kiv module grid.utils.estimate_kiv_dir module grid.utils.extract_reference module grid.utils.find_neighbors module grid.utils.find_neighbors_dir module grid.utils.helper_dir module grid.utils.mosdepth_dir module grid.utils.normalize_mosdepth_dir module grid.utils.run_mosdepth module grid.utils.run_normalized_mosdepth module grid.utils.subset_cram module

L

load_count_results() (in module grid.utils.compute_dipcn_dir) load_dipcn_file() (in module grid.utils.estimate_kiv_dir) load_flags() (in module grid.utils.helper_dir)

load_neighbor_results() (in module grid.utils.compute_dipcn_dir) load_positions() (in module grid.utils.align_lpa_dir) load_reference() (in module grid.utils.align_lpa_dir) load_repeat_mask() (in module grid.utils.normalize_mosdepth_dir)

M

main() (in module grid.cli) merge_exon_data() (in module grid.utils.estimate_kiv_dir) module grid grid.cli grid.config grid.pipeline grid.utils grid.utils.align_lpa grid.utils.align_lpa_dir grid.utils.compute_dipcn grid.utils.compute_dipcn_dir grid.utils.count_reads grid.utils.count_reads_dir grid.utils.ensure_crai grid.utils.estimate_kiv grid.utils.estimate_kiv_dir grid.utils.extract_reference grid.utils.find_neighbors grid.utils.find_neighbors_dir grid.utils.helper_dir grid.utils.mosdepth_dir grid.utils.normalize_mosdepth_dir grid.utils.run_mosdepth grid.utils.run_normalized_mosdepth grid.utils.subset_cram

N

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

normalize_sample_id() (in module grid.utils.compute_dipcn_dir)

P

parse_cigar() (in module grid.utils.align_lpa_dir) print_banner() (in module grid.cli) print_batch_summary() (in module grid.utils.helper_dir) print_individual_error() (in module grid.utils.helper_dir)

print_individual_success() (in module grid.utils.helper_dir) print_version_and_exit() (in module grid.cli) process_cram_file() (in module grid.utils.align_lpa_dir) process_single_cram() (in module grid.utils.count_reads_dir)

R

read_normalized_data() (in module grid.utils.find_neighbors_dir) regions_bed_gz() (in module grid.utils.normalize_mosdepth_dir) run_lpa_realignments() (in module grid.utils.align_lpa)

run_mosdepth() (in module grid.utils.run_mosdepth) run_mosdepth_single_cram() (in module grid.utils.mosdepth_dir) run_normalize_mosdepth() (in module grid.utils.run_normalized_mosdepth)

S

save_neighbors() (in module grid.utils.find_neighbors_dir) select_high_variance_regions() (in module grid.utils.normalize_mosdepth_dir)

setup_output_file() (in module grid.utils.helper_dir) subset_cram() (in module grid.utils.subset_cram)

V

validate_inputs() (in module grid.utils.align_lpa_dir)

validate_sample_overlap() (in module grid.utils.compute_dipcn_dir)

W

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

write_dipcn_output() (in module grid.utils.compute_dipcn_dir) write_normalized_output() (in module grid.utils.normalize_mosdepth_dir) write_result_to_file() (in module grid.utils.helper_dir)