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29 Open 38 Closed
29 Open 38 Closed
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Issues list

Bizarre mamba installation error for a python 3.7.16 environment bug Something isn't working installation Everybody's favorite part of bioinformatics
#70 opened Sep 14, 2023 by fedarko
1
Reject contigs with names that would break bcftools bug Something isn't working good first issue Good for newcomers
#65 opened Jan 26, 2023 by fedarko
Use pyfaidx to access contigs in FASTA files performance gotta go fast
#64 opened Nov 7, 2022 by fedarko
Output un-normalized coverages from "dynam covskew" documentation Improvements or additions to documentation enhancement New feature or request
#63 opened Nov 3, 2022 by fedarko
4 tasks
More efficient contig subsetting enhancement New feature or request performance gotta go fast
#62 opened Oct 29, 2022 by fedarko
Fix CI warnings from GitHub Actions administrative Logistical, non-code-related things testing Plans for future tests, issues with current tests, etc.
#61 opened Oct 25, 2022 by fedarko
Consistent behavior on delaying creation of the output file(s) / output directory backburner Low-priority things that are still good to keep track of
#60 opened Oct 21, 2022 by fedarko
Close BAM files after every command / test that loads them backburner Low-priority things that are still good to keep track of question Further information is requested
#59 opened Oct 19, 2022 by fedarko
Combining downstream commands future ideas longer-term enhancements that'd require a lot of extra time/attention performance gotta go fast
#58 opened Oct 15, 2022 by fedarko
Ensure that contig names can be used within filenames backburner Low-priority things that are still good to keep track of bug Something isn't working
#57 opened Oct 13, 2022 by fedarko
Including (some) rare mutations from the decoy contig in the "fdr fix" BCF? backburner Low-priority things that are still good to keep track of enhancement New feature or request future ideas longer-term enhancements that'd require a lot of extra time/attention
#54 opened Sep 30, 2022 by fedarko
Compress TSV outputs? backburner Low-priority things that are still good to keep track of performance gotta go fast
#53 opened Sep 23, 2022 by fedarko
Replace lists of numbers used for diversity index p / r values with multiple=True? backburner Low-priority things that are still good to keep track of
#51 opened Sep 21, 2022 by fedarko
Output file of "unreasonable position" information during naive calling enhancement New feature or request performance gotta go fast
#48 opened Sep 11, 2022 by fedarko
5 tasks
Smoothed read creation: only (re-)compute average coverages for contigs with > 0 mutations performance gotta go fast
#44 opened Aug 27, 2022 by fedarko
Speed up input BCF validation performance gotta go fast
#43 opened Aug 25, 2022 by fedarko
Warn / fail when we encounter massive datasets? documentation Improvements or additions to documentation notes Not necessarily a single issue, just thoughts on something testing Plans for future tests, issues with current tests, etc.
#37 opened Aug 19, 2022 by fedarko
Parallelizing certain operations future ideas longer-term enhancements that'd require a lot of extra time/attention performance gotta go fast
#36 opened Aug 18, 2022 by fedarko
Warn user if an input BCF contains no mutations across any contigs enhancement New feature or request testing Plans for future tests, issues with current tests, etc.
#35 opened Aug 17, 2022 by fedarko
Notes on overwriting documentation Improvements or additions to documentation notes Not necessarily a single issue, just thoughts on something testing Plans for future tests, issues with current tests, etc.
#34 opened Aug 17, 2022 by fedarko
Support circular GFF3 features in hotspot detection? backburner Low-priority things that are still good to keep track of
#31 opened Aug 11, 2022 by fedarko
3 tasks
Additional minimap2 parameters that are useful for HiFi data backburner Low-priority things that are still good to keep track of enhancement New feature or request
#29 opened Jun 14, 2022 by fedarko
Generalize to multi-allelic mutations future ideas longer-term enhancements that'd require a lot of extra time/attention
#28 opened Jun 13, 2022 by fedarko
Clearer explanation of "rare" / indisputable mutations in the tutorial? documentation Improvements or additions to documentation
#27 opened Jun 6, 2022 by fedarko
Adjusting align to work around indexing limits bug Something isn't working enhancement New feature or request performance gotta go fast
#21 opened Jun 1, 2022 by fedarko
1 of 2 tasks
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