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CRISPRme v2.2.0-alpha.30

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@lucapinello lucapinello released this 18 Aug 00:19
· 28 commits to main since this release

Fixed

  • Indel off-targets were silently dropped since v2.1.9. post_analisi_indel.sh
    subset the per-chromosome indel targets with grep -F -w $chrom, but the indel
    search runs on a per-chromosome fake genome (pool_search_indels.py searches and
    names its targets fake<chrom>), so every indel target row's Chromosome column is
    fake<chrom> (e.g. fakechr22) — which grep -F -w chr22 can never match (-w's
    left word boundary fails because chr22 is preceded by the word character e). The
    per-chromosome subsets came back empty, the indel post-analysis processed nothing,
    and all indel off-targets were dropped with a clean exit. Both grep lines now
    match on "$fakechrom" (-w still prevents fakechr2 matching fakechr22); the
    NF >= 10 malformed-line guard that the same refactor had dropped is restored; and
    an empty subset now prints a WARNING to stdout (stderr is fatal in this pipeline) so
    the failure can never be silent again. A hermetic regression test
    (test_indel_chrom_subset.py) is added and wired into CI. SNP post-analysis is
    unaffected (SNP targets use real chromosome names). Thanks to @munchr-gene1 for the
    report and diagnosis (#172).