35 lines
1.2 KiB
Bash
35 lines
1.2 KiB
Bash
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#!/usr/bin/env bash
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# Usage: simulate_query_one.sh genome.fna.gz output_dir
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# Simulates a fixed-size paired-end HiSeq read set for the query benchmark.
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# Unlike simulate_one.sh (coverage-proportional, used to build the indexed
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# specimens), this always draws N_READS pairs regardless of genome size —
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# query benchmark numbers (wall/RSS) must stay comparable across genomes of
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# very different sizes. Independent iss run (unseeded), so error draw
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# differs from any simulated_data/ reads for the same genome.
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set -euo pipefail
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SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
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ISS="${SCRIPT_DIR}/../.venv/bin/iss"
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N_READS=100000
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CPUS="${CPUS:-$(sysctl -n hw.logicalcpu 2>/dev/null || nproc 2>/dev/null || echo 2)}"
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genome_file="$1"
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out_dir="$2"
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mkdir -p "${out_dir}"
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tmp_fasta=$(mktemp "${TMPDIR:-/tmp}/obikmer_XXXXXX.fna")
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trap 'rm -f "${tmp_fasta}"' EXIT
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gzip -dc "${genome_file}" > "${tmp_fasta}"
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echo "[${out_dir}] ${N_READS} read pairs (query benchmark, fixed size)"
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"${ISS}" generate \
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--genomes "${tmp_fasta}" \
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--model HiSeq \
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--n_reads "${N_READS}" \
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--cpus "${CPUS}" \
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--compress \
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--output "${out_dir}/reads"
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