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Keep a given --min-read-percent-identity in metabat mode - #309
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The metabat method replaced any --min-read-percent-identity with 97%, so a lower threshold was silently ignored. Use 97% only when none is given, and say so in the method's help. Fixes wwood#308 Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
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@codez please review |
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cc @codex |
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Thanks. I ended up fixing some other things along the same lines too. |
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contig --methods metabatreplaced any--min-read-percent-identitywith 97% (#308). With this change, a given threshold is kept, and 97% applies only when none is given. The metabat entry incontig --full-helpnow says so. The secondary, supplementary and improper-pair settings are unchanged.New test
test_metabat_given_percent_identity_is_kept:-m metabat --min-read-percent-identity 90onk141_2005182.head11.bam.-m length mean variance --min-read-percent-identity 90 --min-covered-fraction 0 --contig-end-exclusion 75 --include-secondary.test_metabat_97_of_100_bases_should_failrow exactly (1.9333 / 0.0631).Fixes #308
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