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cutadapt improvements #5577

Merged
merged 23 commits into from
Dec 17, 2023
Merged

cutadapt improvements #5577

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37323d1
cutadapt: fix tests
bernt-matthias Nov 3, 2023
b64b22b
cutadapt: add argument to quality_cutoff2
bernt-matthias Nov 2, 2023
f009d9d
cutadapt: unify adapter specification using macros
bernt-matthias Nov 3, 2023
ed4f20e
cutadapt: replace adapter conditionals by macros
bernt-matthias Nov 3, 2023
7455e58
cutadapt: move cut argument
bernt-matthias Nov 3, 2023
212f0e8
cutadapt: drop internal and unify cli generation for adapter options
bernt-matthias Nov 3, 2023
31365f2
cutadapt: move min/max length for R2 to R2 options
bernt-matthias Nov 3, 2023
510a4af
cutadapt: use checked for bools
bernt-matthias Nov 3, 2023
6f52397
cutadapt: only allow fastqsanger
bernt-matthias Nov 3, 2023
74b5a7f
cutadapt: bump
bernt-matthias Nov 3, 2023
2a48ce1
cutadapt: fix output handling, add polyA trimming arg, bump
bernt-matthias Nov 5, 2023
3a88e60
cutadapt: fix handling of fastqillumina
bernt-matthias Nov 6, 2023
3f40a9a
cutadapt: fix compressed fasta handling
bernt-matthias Nov 6, 2023
8755a68
cutadapt: do not use remote test data
bernt-matthias Nov 6, 2023
33e505e
cutadapt: better regex for quality cutoff param
bernt-matthias Nov 6, 2023
51f9c18
cutadapt: fix --max-expected-errors and add --max-average-error-rate
bernt-matthias Nov 6, 2023
abda5b0
cutadapt: make no_match_adapter_wildcards independent
bernt-matthias Nov 6, 2023
4028432
temporarily disable paired fasta input
bernt-matthias Dec 11, 2023
80df573
fix tests
bernt-matthias Dec 11, 2023
23dd222
Revert "temporarily disable paired fasta input"
bernt-matthias Dec 11, 2023
099aca0
bump to 4.6
bernt-matthias Dec 12, 2023
4c55ba9
fix test data
bernt-matthias Dec 15, 2023
68d7365
use is_of_type instead of ext str comparison
bernt-matthias Dec 17, 2023
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