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.
28 lines
818 B
Bash
Executable File
28 lines
818 B
Bash
Executable File
#!/usr/bin/env bash
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set -euo pipefail
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SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
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BINARY="${SCRIPT_DIR}/../src/target/release/obikmer"
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INDEX="${SCRIPT_DIR}/global_index_presence"
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REF_DIR="${SCRIPT_DIR}/reference_index"
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STATS_DIR="${SCRIPT_DIR}/stats/verify_merge_presence"
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PYTHON="${SCRIPT_DIR}/../.venv/bin/python3"
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VERIFY_PY="${SCRIPT_DIR}/verify_merge_presence.py"
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mkdir -p "${STATS_DIR}"
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CURRENT="${STATS_DIR}/current.csv"
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"${PYTHON}" "${VERIFY_PY}" --header >"${CURRENT}"
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"${PYTHON}" "${VERIFY_PY}" \
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--obikmer "${BINARY}" \
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"${INDEX}" "${REF_DIR}" \
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>>"${CURRENT}"
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run_n=$(printf '%03d' "$(find "${STATS_DIR}" -maxdepth 1 -name 'presence_*.csv' | wc -l | tr -d ' ')")
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ARCHIVE="${STATS_DIR}/presence_${run_n}.csv"
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cp "${CURRENT}" "${ARCHIVE}"
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echo "Done. Results → ${ARCHIVE}"
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