Eric Coissac
c694e1f2b0
Introduces a Make-based orchestration for simulating, indexing, merging, filtering, and verifying k-mer counts and presence. Exposes internal builder and iterator APIs publicly, enforces mandatory leading slashes for predicate patterns, registers the `obitaxonomy` crate, and updates tooling configurations alongside documentation.
13 lines
491 B
Bash
Executable File
13 lines
491 B
Bash
Executable File
#!/usr/bin/env bash
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# Simulate all genomes. Delegates to simulate_one.sh per genome.
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# Prefer running via `gmake simulate` which handles individual dependencies.
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set -euo pipefail
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SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
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for genome_file in "${SCRIPT_DIR}"/genomes/*.fna.gz; do
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out_dir=$("${SCRIPT_DIR}/../.venv/bin/python3" "${SCRIPT_DIR}/make_deps.py" \
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--dir-for "${genome_file}")
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bash "${SCRIPT_DIR}/simulate_one.sh" "${genome_file}" "${out_dir}"
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done
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