v2.3.0 PR - #116

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BioWilko wants to merge 19 commits into

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beeeeg-optimisation-pass

Commits on Aug 27, 2026

Large number of small optimisation changes
BioWilko
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8dacd9c
bump version tag
BioWilko
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a928345
Move from bgzip to pigz
BioWilko
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522e423
Fast exit check_reads for long read data, the iteration is intolerably slow to account for an extremely rare failcase
BioWilko
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107fa3d
revert to tmpfile for FASTQs, piping slow for some reason
BioWilko
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e023b10
Move to crabz for faster gzip compression
BioWilko
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7f2a52f
bump container tag
BioWilko
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dc95780
Move to wave container for scylla
BioWilko
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a1154e2
Fix taxon ordering bug
BioWilko
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6dc2973
Handle secondary ranks (e.g. G1) consistently
BioWilko
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c727c92
Output simple rank rather thank full rank
BioWilko
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7809cd6

Commits on Aug 28, 2026

increase label for mm2_hcid
BioWilko
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f3f24a3
bump extract taxa label
BioWilko
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25b7063
further optimise hcid/extract fractions logic
BioWilko
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97c6358
Migrate to rammap for alignment
BioWilko
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4070fe1
bump extract reads labels
BioWilko
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111995a
give check hcid more memory
BioWilko
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d0914cc

Commits on Sep 1, 2026

Further fixes
BioWilko
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208d473

Commits on Sep 10, 2026

default taxa by rank filter to species not serotype
BioWilko
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b12b627