Fix 10 bugs affecting new VCF dataset processing, concurrent runs, and gnomAD conversion by anncir1 · Pull Request #96 · pinellolab/CRISPRme

Fix BLANK_LINE_IN_SAMPLES_FILE: skip blank lines in init_summary_by_sample()

anncir1

committed

Fix CHR_FROM_FILENAME: read chromosome from VCF content, not filename

anncir1

committed

Fix FILTER_PASS: add --vcf-filter-pass-values flag (default "PASS,.")

anncir1

committed

Fix GT_HAPLOID: guard against bare 0/1 haploid GT (no | separator)

anncir1

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Fix CONCURRENT_RUNS: unique temp dir and mkdir locks for shared build steps

anncir1

committed

Fix DTYPE_WARNING: add dtype=str to chunked pd.read_csv in remove_n_and_dots

anncir1

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Fix CHR_FROM_FILENAME: normalize chr prefix after _chrom_from_vcf()

anncir1

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Fix TBI_FILTER: exclude .vcf.gz.tbi files from chromosome list in pool_post_analisi_indel

anncir1

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Fix TABIX_CONCURRENT_WRITE: only regenerate .tbi when absent to prevent parallel write race

anncir1

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Fix TABIX_CONCURRENT_WRITE: flock + timestamp check replaces bare existence check

anncir1

committed

Fix FILTER_PASS: remove VCF rewrite loop from submit_job

anncir1

committed

Fix MISSING_ALLELE: guard against '.' alleles in resultIntegrator haplotype counting

anncir1

committed

Fix GT_HAPLOID (extension): add haploid guard to new_simple_analysis.py

anncir1

committed

Fix GNOMAD_CONVERTER: add --af-threshold and --output-dir flags; fix AF field lookup

anncir1

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Fix 10 bugs affecting new VCF dataset processing, concurrent runs, and gnomAD conversion#96

Fix 10 bugs affecting new VCF dataset processing, concurrent runs, and gnomAD conversion#96
anncir1 wants to merge 14 commits into
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ac/vcf-fixes

Commits on Apr 10, 2026

Fix BLANK_LINE_IN_SAMPLES_FILE: skip blank lines in init_summary_by_sample()

Fix CHR_FROM_FILENAME: read chromosome from VCF content, not filename

Fix FILTER_PASS: add --vcf-filter-pass-values flag (default "PASS,.")

Fix GT_HAPLOID: guard against bare 0/1 haploid GT (no | separator)

Fix CONCURRENT_RUNS: unique temp dir and mkdir locks for shared build steps

Fix DTYPE_WARNING: add dtype=str to chunked pd.read_csv in remove_n_and_dots

Fix CHR_FROM_FILENAME: normalize chr prefix after _chrom_from_vcf()

Fix TBI_FILTER: exclude .vcf.gz.tbi files from chromosome list in pool_post_analisi_indel

Fix TABIX_CONCURRENT_WRITE: only regenerate .tbi when absent to prevent parallel write race

Fix TABIX_CONCURRENT_WRITE: flock + timestamp check replaces bare existence check

Fix FILTER_PASS: remove VCF rewrite loop from submit_job

Fix MISSING_ALLELE: guard against '.' alleles in resultIntegrator haplotype counting

Fix GT_HAPLOID (extension): add haploid guard to new_simple_analysis.py

Fix GNOMAD_CONVERTER: add --af-threshold and --output-dir flags; fix AF field lookup