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rki-mf1
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covsonar
A database-driven system for handling genomic sequences of SARS-CoV-2 and screening genomic profiles.
GNU General Public License v3.0
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Bump conda-incubator/setup-miniconda from 3.0.4 to 3.1.0
#129
dependabot[bot]
opened
4 weeks ago
0
Bump psf/black from 24.8.0 to 24.10.0
#128
dependabot[bot]
opened
1 month ago
0
Bump psf/black from 24.4.2 to 24.8.0
#127
dependabot[bot]
closed
2 months ago
0
Bump actions/checkout from 3 to 4
#126
dependabot[bot]
closed
5 months ago
0
Bump psf/black from 23.10.1 to 24.4.2
#125
dependabot[bot]
closed
5 months ago
0
Bump conda-incubator/setup-miniconda from 2.1.1 to 3.0.4
#124
dependabot[bot]
closed
5 months ago
0
Allow match query parameters to be read from a file
#123
matthuska
closed
1 year ago
1
If match returns no rows, still output column names
#122
matthuska
closed
1 year ago
0
Automatically update parent-child lineage info
#121
matthuska
closed
1 year ago
0
Switch to nextstrain SARS-CoV-2 gene annotation as default
#120
matthuska
opened
1 year ago
0
Update lineage information whenever a user does a match query with sublineages
#119
matthuska
closed
1 year ago
0
Check formatting with black on push or pull requests
#118
matthuska
closed
1 year ago
0
Reformat code using black + zimports. Fix file endings. Remove execute bit.
#117
matthuska
closed
1 year ago
0
Add covsonar 1 precommit hook to run black and zimports, etc.
#116
matthuska
closed
1 year ago
0
Allow matching by seqhash (including negation with '^')
#115
matthuska
closed
1 year ago
0
Fix match command
#114
silenus092
closed
5 months ago
6
Don't crash when filtering empty profile. Closes #112
#113
matthuska
closed
1 year ago
0
Match query fails with AttributeError: 'NoneType' object has no attribute 'split'
#112
matthuska
closed
1 year ago
0
Import cache takes up a lot of disk space
#111
matthuska
closed
1 year ago
2
Rewrite property handling to use a simple table rather than an entity-attribute-value table
#110
matthuska
closed
1 year ago
4
[test] show current incorrect results when match querying two properties
#109
matthuska
closed
1 year ago
0
GISAID sequences cause errors when importing into a database
#108
matthuska
closed
1 year ago
2
refix: avoid deletion of identical sequences
#107
stephan-fuchs
closed
1 year ago
0
Sublineage queries silently fail when `update-lineages` has never been run for a database
#106
matthuska
closed
1 year ago
1
"pango" property type not document in README.md
#105
matthuska
closed
1 year ago
2
Allow lineages to also be updated from local files
#104
matthuska
closed
1 year ago
0
Avoid bug when deleting sequences which are identical to others
#103
matthuska
closed
1 year ago
0
Match by `seqhash`
#102
MarieLataretu
closed
1 year ago
0
Fix matching on multiple properties and profiles
#101
matthuska
closed
1 year ago
1
Broken pipe error on using `head` on output of `match` command
#100
matthuska
opened
1 year ago
0
Initial table with all commands we are using regularly from covsonar 1
#99
matthuska
closed
1 year ago
1
covsonar 2 runtime (and memory usage?)
#98
matthuska
closed
1 year ago
2
Explain differences in DNA, AA and frameshift profiles between covsonar 1 and covsonar 2
#97
matthuska
closed
1 year ago
2
Ensure all currently needed covsonar 1 commands are present in covsonar 2 and how to switch is documented
#96
matthuska
closed
1 year ago
1
Add --only-frameshifts and --no-frameshifts arguments
#95
matthuska
closed
1 year ago
1
Option to output all unique elements of a given metadata field
#94
matthuska
opened
1 year ago
0
Add workflow diagram to README
#93
matthuska
opened
1 year ago
0
Optionally mask the start/end of sequences
#92
matthuska
opened
1 year ago
0
Stats about blind spots (N) when matching genomic profiles
#91
matthuska
opened
1 year ago
0
Match accessions by list of accessions in a file
#90
MarieLataretu
closed
1 year ago
2
Special case for properties starting in '.', lstrip() them.
#89
matthuska
closed
1 year ago
0
Bump package and tooling dependencies
#88
matthuska
closed
1 year ago
2
zimports: split imports over multiple lines
#87
matthuska
closed
1 year ago
0
--only_frameshifts reports empty files, if none found
#86
oliverdrechsel
closed
1 year ago
0
CovSonar crashes with: sqlite3.OperationalError: attempt to write a readonly database
#85
fischer-hub
closed
1 year ago
2
VCF file restored from covsonar and Usher pre-processing
#84
Achilleas-Galanopoulos
closed
1 year ago
1
covsonar2.alpha-3 for testing
#83
silenus092
closed
1 year ago
0
Error when extracting TSV from rki.db 2021-12-07
#82
hoelzer
closed
1 year ago
7
Error when extracting a certain lineage
#81
hoelzer
closed
1 year ago
6
Update of a sequence identical to another deletes mutation profile of the other sequence
#80
paulwolk
closed
1 year ago
4
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