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--acc2tax CLI-config command line option --add-fit-predictions CLI-convert command line option CLI-filter command line option --bayesian CLI-config command line option --config-file CLI-config command line option --cores-per-sample CLI-config command line option --custom-database CLI-config command line option --damage-mode CLI-config command line option --debug CLI-dashboard command line option --force CLI-compute command line option --forward-only CLI-config command line option --host CLI-dashboard command line option --install-completion CLI command line option --lca-rank CLI-config command line option --long-name CLI-config command line option --max-edit-dist CLI-config command line option --max-position CLI-config command line option --max-similarity-score CLI-config command line option --metaDMG-cpp CLI-config command line option CLI-PMD command line option --min-edit-dist CLI-config command line option --min-mapping-quality CLI-config command line option --min-reads CLI-config command line option --min-similarity-score CLI-config command line option --names CLI-config command line option --nodes CLI-config command line option --output CLI-convert command line option CLI-filter command line option CLI-mismatch-to-mapDamage command line option CLI-plot command line option CLI-PMD command line option --output-dir CLI-config command line option CLI-get-data command line option --overwrite CLI-config command line option --parallel-samples CLI-config command line option --port CLI-dashboard command line option --query CLI-filter command line option CLI-plot command line option --results CLI-convert command line option CLI-dashboard command line option CLI-filter command line option CLI-plot command line option --sample-prefix CLI-config command line option --sample-suffix CLI-config command line option

--samples CLI-plot command line option --server CLI-dashboard command line option --show-completion CLI command line option --tax-ids CLI-plot command line option --version CLI command line option --weight-type CLI-config command line option -a CLI-convert command line option CLI-filter command line option -b CLI-config command line option -c CLI-config command line option -d CLI-config command line option CLI-dashboard command line option -E CLI-config command line option -e CLI-config command line option -f CLI-compute command line option CLI-config command line option -h CLI-dashboard command line option -i CLI-config command line option -j CLI-config command line option -l CLI-config command line option -m CLI-config command line option CLI-PMD command line option -n CLI-config command line option -o CLI-config command line option CLI-convert command line option CLI-filter command line option CLI-get-data command line option CLI-mismatch-to-mapDamage command line option CLI-plot command line option CLI-PMD command line option -P CLI-config command line option -p CLI-dashboard command line option -q CLI-config command line option CLI-filter command line option CLI-plot command line option -r CLI-config command line option CLI-convert command line option CLI-dashboard command line option CLI-filter command line option CLI-plot command line option -S CLI-config command line option -s CLI-config command line option CLI-dashboard command line option CLI-plot command line option -t CLI-plot command line option -u CLI-config command line option -v CLI command line option -w CLI-config command line option

C

check_number_of_jobs() (metaDMG.utils.Configs method) CLI command line option --install-completion --show-completion --version -v CLI-compute command line option --force -f CONFIG_FILE CLI-config command line option --acc2tax --bayesian --config-file --cores-per-sample --custom-database --damage-mode --forward-only --lca-rank --long-name --max-edit-dist --max-position --max-similarity-score --metaDMG-cpp --min-edit-dist --min-mapping-quality --min-reads --min-similarity-score --names --nodes --output-dir --overwrite --parallel-samples --sample-prefix --sample-suffix --weight-type -b -c -d -e -E -f -i -j -l -m -n -o -P -q -r -s -S -u -w SAMPLES CLI-convert command line option --add-fit-predictions --output --results -a -o -r CONFIG_FILE

CLI-dashboard command line option --debug --host --port --results --server -d -h -p -r -s CONFIG_FILE CLI-filter command line option --add-fit-predictions --output --query --results -a -o -q -r CONFIG_FILE CLI-get-data command line option --output-dir -o CLI-mismatch-to-mapDamage command line option --output -o FILENAME CLI-plot command line option --output --query --results --samples --tax-ids -o -q -r -s -t CONFIG_FILE CLI-PMD command line option --metaDMG-cpp --output -m -o FILENAME compute_config() (in module metaDMG.main) Config (class in metaDMG.utils) CONFIG_FILE CLI-compute command line option CLI-convert command line option CLI-dashboard command line option CLI-filter command line option CLI-plot command line option Configs (class in metaDMG.utils)

F

FILENAME CLI-mismatch-to-mapDamage command line option CLI-PMD command line option

G

get_first() (metaDMG.utils.Configs method)

get_nth() (metaDMG.utils.Configs method) get_results_dir() (in module metaDMG.utils)

L

load_results() (in module metaDMG.main)

M

make_configs() (in module metaDMG.utils) metaDMG.main module metaDMG.utils module

module metaDMG.main metaDMG.utils

R

remove_directory() (in module metaDMG.utils)

run_dashboard() (in module metaDMG.main) run_PMD() (in module metaDMG.utils)

S

SAMPLES CLI-config command line option

split_string() (in module metaDMG.utils)