Eric Coissac
54e4600120
Introduces a `batch_int_group_stats` API for computing presence counts, sums, minimums, and maximums across sparse and dense matrix representations. The selection layer now utilizes this batched approach to optimize aggregation semantics for boolean and numeric operations. Additionally, reorganizes the benchmarking infrastructure to support querying across presence and count index variants in both dense and sparse formats, including new packing scripts and updated statistics aggregation.
29 lines
852 B
Bash
Executable File
29 lines
852 B
Bash
Executable File
#!/usr/bin/env bash
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# Usage: verify_query_one.sh SPECIMEN
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# SPECIMEN = "species--strain" (Make pattern stem)
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# Output: stats/verify_query/SPECIMEN.stats (one CSV data row, no header)
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set -euo pipefail
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SPECIMEN="$1"
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SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
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PYTHON="${SCRIPT_DIR}/../.venv/bin/python3"
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VERIFY_PY="${SCRIPT_DIR}/verify_query.py"
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species="${SPECIMEN%%--*}"
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strain="${SPECIMEN#*--}"
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DENSE="${SCRIPT_DIR}/query_presence_dense/${SPECIMEN}.fasta.gz"
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SPARSE="${SCRIPT_DIR}/query_presence_sparse/${SPECIMEN}.fasta.gz"
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STATS_DIR="${SCRIPT_DIR}/stats/verify_query"
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STATS_FILE="${STATS_DIR}/${SPECIMEN}.stats"
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mkdir -p "${STATS_DIR}"
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echo "[${SPECIMEN}] verifying query (dense vs sparse)"
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"${PYTHON}" "${VERIFY_PY}" \
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--species "${species}" \
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--strain "${strain}" \
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"${DENSE}" "${SPARSE}" \
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>"${STATS_FILE}"
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