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40 Open 155 Closed
40 Open 155 Closed
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Issues list

Propagation make clean – use xargs instead of -exec with find
#398 opened Mar 14, 2024 by karel-brinda
Verify ProPhyle bioconda dependencies
#395 opened Dec 7, 2023 by karel-brinda
Index propagation Makefile cannot deal with spaces in parental dirs bug cmd:index
#376 opened May 18, 2022 by karel-brinda
Remove prophyle_index_footprint (redundant)
#367 opened Aug 17, 2021 by karel-brinda
Use xopen for opening files enhancement
#366 opened Aug 16, 2021 by karel-brinda
When the number of input files is large, prophyle index check is too slow
#355 opened Aug 9, 2021 by karel-brinda
Automatic autocompletion does weird things with the tree bug
#343 opened Jul 30, 2021 by karel-brinda
1
Manual compilation of BWA bug
#342 opened Mar 8, 2021 by karel-brinda
3
If a dataset fully contained, make a single fake sequence of legth 1 enhancement
#341 opened Oct 14, 2020 by karel-brinda
Add times to logs in order to simply tuning on clusters enhancement
#339 opened Oct 10, 2020 by karel-brinda
Bacterial library contains archaeal genomes bug cmd:download high importance
#332 opened Apr 10, 2019 by nataquinones
@simonepignotti
1
When processing of a read fails, add read name to the error message enhancement
#331 opened Feb 27, 2019 by karel-brinda
Don't pass default options to prophex and assignment enhancement
#330 opened Feb 13, 2019 by karel-brinda
Embed tree into the output bam feature request
#327 opened Jan 23, 2019 by karel-brinda
1 task
1
prophyle-classify: Add a parameter for propagating assignments to the leaf level feature request prophyle_assignment
#325 opened Aug 8, 2018 by karel-brinda
@karel-brinda
prophyle compress: Add a cli parameter for specifying a tmp dir enhancement
#321 opened Jun 20, 2018 by karel-brinda
prophyle_assignment: not enough values to unpack (expected 2, got 1) bug
#320 opened Jun 1, 2018 by karel-brinda
4
Cluster sync lantencies => prophyle_propagation_postprocessing.py: FileNotFoundError: [Errno 2] No such file or directory bug
#319 opened May 31, 2018 by karel-brinda
Parallelize classification cmd:classify enhancement
#311 opened May 15, 2018 by simonepignotti
Compute k-mer statistics in non-propagation mode bug low importance
#309 opened May 9, 2018 by simonepignotti
1
Propagation: include k in the file names cmd:index enhancement
#296 opened Apr 13, 2018 by karel-brinda
Add an option for masking unmatched bases feature request
#293 opened Jan 2, 2018 by karel-brinda
prophyle download: Add an option to specify a version of DB cmd:download enhancement
#286 opened Nov 20, 2017 by karel-brinda
@karel-brinda
Autodetect autocompletion enhancement
#285 opened Nov 14, 2017 by karel-brinda
Double check manually results of test A10_krakenlike_results tests
#273 opened Oct 8, 2017 by karel-brinda
4 tasks
1
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