CRISPRme v2.2.0-alpha.30
Pre-release
Pre-release
·
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 withgrep -F -w $chrom, but the indel
search runs on a per-chromosome fake genome (pool_search_indels.pysearches and
names its targetsfake<chrom>), so every indel target row's Chromosome column is
fake<chrom>(e.g.fakechr22) — whichgrep -F -w chr22can never match (-w's
left word boundary fails becausechr22is preceded by the word charactere). The
per-chromosome subsets came back empty, the indel post-analysis processed nothing,
and all indel off-targets were dropped with a clean exit. Both grep lines now
match on"$fakechrom"(-wstill preventsfakechr2matchingfakechr22); the
NF >= 10malformed-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).