MatthewRalston kmerdb issues

MatthewRalston / kmerdb

Python bioinformatics CLI for k-mer counts and de Bruijn graphs

https://matthewralston.github.io/kmerdb

Apache License 2.0

12 stars 1 forks source link

issues

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Regression in 0.8.6, possilby 0.8.5. parse no longer uses deprecated option 'b' for fastq block size. Acceptance test details follow

#154 MatthewRalston closed 3 months ago
0
Graph node labeling and traversal update

#153 MatthewRalston opened 3 months ago
0
Kolmogorov complexity

#152 MatthewRalston opened 3 months ago
0
Notes on mouse ibd

#151 MatthewRalston opened 3 months ago
0
Profile recomposition problem

#150 MatthewRalston opened 3 months ago
2
Quarto template an app. note

#149 MatthewRalston opened 3 months ago
0
Bump certifi from 2024.6.2 to 2024.7.4

#148 dependabot[bot] opened 3 months ago
1
Bump urllib3 from 2.2.1 to 2.2.2

#147 dependabot[bot] opened 3 months ago
1
Bump scikit-learn from 1.0.2 to 1.5.0

#146 dependabot[bot] opened 3 months ago
1
Solution engineering for disease model mutational model discrete probabilities. What...

#144 MatthewRalston closed 4 months ago
0
.kdbg format and variants

#143 MatthewRalston opened 4 months ago
4
Expectation functions

#142 MatthewRalston opened 4 months ago
1
D2 metrics

#141 MatthewRalston opened 4 months ago
0
Tetranucleotide bias and Karlin delta

#140 MatthewRalston opened 4 months ago
0
Review formulations and Python environment issues

#139 MatthewRalston closed 4 months ago
1
Interface revision, version bump, minor regressions. Tested

#138 MatthewRalston closed 7 months ago
0
README 2.0

#137 MatthewRalston opened 7 months ago
2
Stderr logging - cleanup only

#136 MatthewRalston closed 7 months ago
0
Removing loose-ly deprecated parameters

#135 MatthewRalston closed 7 months ago
2
Kmer.shred always returns sparse kmer_id/count array

#134 MatthewRalston opened 7 months ago
2
New issue 'appmap' (stderr, logger, plain-txt stdout, file outputs, rich formatting if/when necessary)

#133 MatthewRalston closed 7 months ago
2
stderr logging and interface cleanup

#132 MatthewRalston opened 7 months ago
2
vsearch conda package

#131 MatthewRalston opened 7 months ago
1
Expanded row metadata for graph format

#130 MatthewRalston opened 8 months ago
3
Edge list writer still unspecified. Edge list generator undergoing interface overhaul. ,

#129 MatthewRalston closed 8 months ago
1
yaml representer

#128 MatthewRalston closed 7 months ago
1
regression in unique_nullomer + unique_kmers vs 4^k calculation during metadata aggregation across inputs

#127 MatthewRalston closed 4 months ago
1
Interface updates planned, logging rework, and bugfixes. ouch.

#126 MatthewRalston closed 8 months ago
3
still no dl

#125 MatthewRalston opened 8 months ago
3
3-tuple i think

#124 MatthewRalston closed 8 months ago
0
Assert subsequent shredded kmers are neighborly, skip if fails (fastq centered)

#123 MatthewRalston opened 8 months ago
7
Maybe take a walk?

#122 MatthewRalston opened 9 months ago
4
if handle is none in fileutil, produces uncaught exception. Fixed with NoneType conditional

#121 MatthewRalston closed 9 months ago
0
Deprecated feature col3 revisited, affects kmerdb view.

#120 MatthewRalston closed 9 months ago
0
v0.7.5 - fixes minor regressions, --sorted truthiness, ignored --quiet in conditional branch, and fixes duplicate col2 among others

#119 MatthewRalston closed 9 months ago
0
__init__.py --all-metadata has print statement when not --quiet doesn print to stderr the metadata for debugging.

#118 MatthewRalston opened 9 months ago
0
Large regression in __init__.py L1288-1292ish where row number used as index

#117 MatthewRalston closed 9 months ago
1
"truth-ey" argument.sorted in __init__.py#L1214

#116 MatthewRalston closed 9 months ago
1
kmerdb profile --quiet argument ignored on __init__.py#L1214

#115 MatthewRalston closed 9 months ago
1
__init__.py has duplicate storage of kmerid [smell]

#114 MatthewRalston opened 9 months ago
0
kmerdb profile sort order returns improperly sorted col2, col3

#113 MatthewRalston opened 9 months ago
0
twizza project template

#112 MatthewRalston opened 1 year ago
0
Bump ipython from 7.16.3 to 8.10.0

#111 dependabot[bot] closed 3 months ago
1
Hotfix for __init__.py locating CITATION.txt

#110 MatthewRalston closed 1 year ago
0
kmerdb/__init__.py requires CITATION.txt instead of CITATION on L1324-1325

#109 MatthewRalston closed 1 year ago
0
Revert "Fix to pyproject.toml, MANIFEST.in, setup.py setup.cfg and build stack"

#108 MatthewRalston closed 1 year ago
0
Fix to pyproject.toml, MANIFEST.in, setup.py setup.cfg and build stack

#107 MatthewRalston closed 1 year ago
0
Downgrade requirements.txt for some reason...

#106 MatthewRalston closed 1 year ago
0
Downgrade numpy version number.

#105 MatthewRalston closed 1 year ago
0
Fixed documentation, but pyproject.toml installation via PyPI is still expected to be bugged.

#103 MatthewRalston closed 1 year ago
0