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During automated test runs, BTE sometimes raises this error: `TypeError: Cannot read properties of undefined (reading 'endsWith') while configuring query.`Then, BTE appears to skip constructing some s…
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Hi Steven
When using the predict.phenotype function of pypgx v.0.25.0, it often returns Indeterminate phenotypes for wild type diplotypes(*1/*1), while the *1 is defined as a "Normal Function" alle…
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We are interested in using pypgx to call star alleles, but (in one scenario) we do not want to report star alleles that have Unknown or Uncertain function. For example, if a sample was called CYP2D6 *…
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* **Do you want to request a *feature* or report a *bug*?**
feature
* **What is the current behavior?**
reporter.BadOutsideCallException when outside CYP2D6 genotype call is an invalid fo…
songx updated
3 weeks ago
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@PavelBal There are still a lot of high level features undocumented in the toolbox. When can you start working on this
@Yuri05 What features should be outlined in the vignettes?
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More specifically, diplotypes
- `*1x≥3/*41x3`
- `*2x≥3/*41x3`
currently have
- "generesult": "Indeterminate"
- "lookupkey": "n/a"
- "activityScore": "n/a"
- "phenotype": "Indeterminate"
…
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I used `/opt/conda/bin/pbstarphase diplotype -v --normalize-d6-only --bam "${output_dir}/${file}" -d "${CPIC_JSON_DB}" -t 4 -o "${output_dir}/${file}.json" --pharmcat-tsv "${output_dir}/pharmcat.tsv" …
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Hi @GemmaTuron,
In the `data` folder there are `all_molecules_$MODEL_ID.csv` files that I calculated
I suggest we do the following plots using a Jupyter Notebook:
1. A histogram or density p…
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Hi,
I have been running the `pypgx run-ngs-pipeline` in a loop for many genes, including NAT2. I have processed the same samples multiple times (for testing purposes) and I have not had a problem w…
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```
[2024-05-15T21:56:41.601Z DEBUG pbstarphase::cyp2d6_caller] Searching A00297:51:HFM5LDSXX:1:2344:6325:12727 at 42127132
[2024-05-15T21:56:41.618Z DEBUG pbstarphase::data_types::cyp2d6_typer] Col…