rki-mf1 / covsonar

A database-driven system for handling genomic sequences of SARS-CoV-2 and screening genomic profiles.

rki-mf1/covsonar Issues

Switch to nextstrain SARS-CoV-2 gene annotation as default
Updated 10 months ago
Update lineage information whenever a user does a match query with sublineages
Closed 10 months ago
Match query fails with AttributeError: 'NoneType' object has no attribute 'split'
Closed a year ago
Import cache takes up a lot of disk space
Closed 10 months ago2
GISAID sequences cause errors when importing into a database
Closed 10 months ago2
Sublineage queries silently fail when `update-lineages` has never been run for a database
Closed 10 months ago1
"pango" property type not document in README.md
Closed 10 months ago2
Match by `seqhash`
Closed 10 months ago
Broken pipe error on using `head` on output of `match` command
Updated 2 months ago
covsonar 2 runtime (and memory usage?)
Closed 10 months ago2
Explain differences in DNA, AA and frameshift profiles between covsonar 1 and covsonar 2
Closed a year ago2
Ensure all currently needed covsonar 1 commands are present in covsonar 2 and how to switch is documented
Closed 10 months ago1
Add --only-frameshifts and --no-frameshifts arguments
Closed 10 months ago1
Option to output all unique elements of a given metadata field
Updated a year ago
Add workflow diagram to README
Updated a year ago
Optionally mask the start/end of sequences
Updated a year ago
Stats about blind spots (N) when matching genomic profiles
Updated a year ago
Match accessions by list of accessions in a file
Closed 10 months ago2
--only_frameshifts reports empty files, if none found
Closed 10 months ago
CovSonar crashes with: sqlite3.OperationalError: attempt to write a readonly database
Closed a year ago2
VCF file restored from covsonar and Usher pre-processing
Closed a year ago1
Error when extracting TSV from rki.db 2021-12-07
Closed 10 months ago7
Error when extracting a certain lineage
Closed a year ago6
Update of a sequence identical to another deletes mutation profile of the other sequence
Closed a year ago4
querying for a specific mutation returns also genomes that do not contain this mutation
Closed 10 months ago6
--platform not working
Closed a year ago1
Allow to select output columns
Closed 2 years ago2
Fix parent-child construction script
Closed 2 years ago
Decrease memory usage when outputting mutation profiles from large databases
Closed a year ago1
Information on NNNNN stretches
Closed a year ago1
--no_frameshifts does not work with --tsv
Closed 2 years ago
Dev/cov2 mpire - [merged]
Closed 2 years ago1
Restore sequence from file does not work
Closed 2 years ago
Exact match for ANY character in match condtion.
Closed 2 years ago1
Update to [covSonar 1.1.4] - [merged]
Closed 2 years ago3
HotFix - [merged]
Closed 2 years ago1
SQL not working properly - Searching Any Mutation
Closed 2 years ago3
We need to talk about deletions ...
Closed a year ago1
Update to [covSonar 1.1.3] - [merged]
Closed 2 years ago10
Incorrect syntax in where clause (Query NOT on date column is not working)
Closed 2 years ago
build database fails due to non-unique entries in fasta
Closed 2 years ago2
include date of submission in output
Closed 2 years ago
Update to [covSonar V.1.1.2] - [merged]
Closed 2 years ago10
CovSonar fails when reference gff includes features from reverse strand
Closed a year ago
Dev delete function - [merged]
Closed 2 years ago6
Mutation search returns less sequences than previous search
Closed 2 years ago1
Dev/v.1 - [merged]
Closed 2 years ago1
Fix and Add features - [merged]
Closed 2 years ago4
Zero length Hot Fix - [merged]
Closed 2 years ago1
Get results for any AA substitution does not work
Closed 2 years ago1