kemal
7fb3967c3f
- tests/unit/test_genotype.py: fuzzy memberships incl. NaN rules, calls at cluster centres, intensity threshold, BAF/LRR interpolation and NaN pattern, LogR-dev locus set, sex rules v1/v2, TOP-strand base calls, invariant dates, end-to-end `simurg genotype` (summary schema, pass-through columns, thread/layout determinism, overwrite refusal) - tests/oracle/test_p4_genotype.py: 36 GSA samples x 2 versions byte-identical to the oracle - scripts/validate_p4_large.py + cloud task p4: compare every vendor GTC field by field and as whole files; reports which sex rule matches
14 lines
747 B
Bash
Executable File
14 lines
747 B
Bash
Executable File
#!/bin/bash
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# Phase P4: genotype every Omni2.5 IDAT pair and compare the GTC with the vendor's (fields + whole file).
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# Args: <data dir with bpm/egt and data/> <results dir>
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set -uo pipefail
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D=$1; OUT=$2
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SRC=s3://1000genomes/release/20130502/supporting/hd_genotype_chip/broad_intensities
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mkdir -p $D/egt
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aws s3 cp --no-sign-request "$SRC/HumanOmni2.5-4v1-Multi_H.egt" $D/egt/ --only-show-errors
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cp $D/HumanOmni2.5-4v1-Multi_B.egt $D/egt/
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/usr/bin/time -v .venv/bin/python scripts/validate_p4_large.py --root $D/data --bpm $D/HumanOmni2.5-4v1-Multi_B.bpm \
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--egt-dir $D/egt --out $OUT/summary.json --norm-version 1.1.2 --sex-version 1 --workers "$(nproc)" \
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2> $OUT/time.txt || echo "P4 validation reported differences"
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tail -25 $OUT/time.txt
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