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This new property was added a few months ago but there is no mention of it in the README.md. I think that using the "text" type for lineages will cause sublineage queries to not work, so this should b…
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When importing data, covsonar "caches" all relevant information in files on the filesystem before doing alignment and ultimately adding the data to the database. This cache can be significantly larger…
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When using e.g.,
`
sonar.py match -db db -i S:R346X --lineage BA.5.3 --with-sublineage`
among the returned genomes there are some which do not contain the R346X mutation.
In the above exampl…
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```
EPI_ISL_17832520
EPI_ISL_17832518
EPI_ISL_17832276
EPI_ISL_15492846
EPI_ISL_15492845
EPI_ISL_15492843
```
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1) Have to exactly identical sequences & with mutations in the database.
2) Sequence gets an update and has a new sequence, so I add it with the "force" flag to overwrite the old sequence.
3) is…
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In GitLab by @s.fuchs on Jun 3, 2021, 07:45
For the next feature updates, I wolud like to collect here some points. Feel free to add your suggestions!
- [x] gz/xz input file support when adding fast…
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Hi,
we ran into an issue where covsonar crashes with :
```
Traceback (most recent call last):
File ".../sc2-autopilot2/lib/covsonar/sonar.py", line 466, in
dbm.check_db_compatibility()…
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Hey,
ORF1ab is a bit complicated due to a Frameshift region that results in two products: ORF1a and ORF1b.
Covsonar outputs duplicate entries and thus they also appear in your matrix, e.g.…
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In GitLab by @oliverdrechsel on Jun 22, 2021, 09:38
it seems a few frameshift variants that are detected by GISAID stay unnoticed by covsonar (or i used it wrong).
```
tools/covsonar/sonar.py --ver…
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In GitLab by @hoelzer on Jan 18, 2022, 13:02
... this is a general problem. It happens quite often, that we search for certain deletions reported in the literature but can not be certain that these …