Lena Schimmel

What about non-BA.1-variants of Omicron?

5

Currently only cases with `lineage == 'BA.1'` are counted as Omicron (see [source](https://github.com/corneliusroemer/desh-data/blob/7381c50e134a8280b4bebfc154adc2d51a8b95ef/scripts/omicron_plot.py#L49)). There are some cases with lineage `BA.2`, `BA.3` or just `B.1.1.529`. Shouldn't they be counted as well?...

Skip special files to avoid NPR in RockerUtil.listFileTree()

1

This should fix fizzed#159.

Generation crashes with NPE if a non-normal file is present in the template directory

1

The method [RockerUtil.listFileTree](https://github.com/fizzed/rocker/blob/4a8d6f11eaf2fb573ba3c142fe4b1464823f24fa/rocker-compiler/src/main/java/com/fizzed/rocker/compiler/RockerUtil.java#L160) throws a `NullPointerException` if there is any file within the template directory which is neither a "normal file" (as defined by [`File.isFile()`](https://docs.oracle.com/javase/7/docs/api/java/io/File.html#isFile())) nor a directory. In my...

Put generated output in its own folder(s)

5

Using this tool on a large twitter that existed for some years account generates a lot of `*-Tweet-Archive-*.md` files, and now that DMs and group DMs are processed, also a...

More work on `downloadtweets`

5

Here's some work which I already did 3 days ago, but had not made into a PR before. Yesterday I incorporated the newest stuff from `timhutton/twitter-archive-parser/main` into both `timhutton/twitter-archive-parser/downloadtweets` and...

Draft not ready for merging. What I did: * Add `create_path_for_file_` methods in `PathConfig` and use them * Add small helper methods `open_and_mkdirs`, `mkdirs_for_file` and `rel_url` * Move class `PathConfig`...

Base feature: Download tweets which are missing or incomplete

4

We have several issues that can only be solved if we download some additional tweets: * #72 * #73 * #39 * #20 * #22 I already started working on...

[Question] Is it expected to take more then 24h to download bookmarks?

2

First of all, I'm very happy that this tool exists and with how reliable it's working. It's currently running on my machine since more than 24 hours, and still working....

I was contacted by @maciekboni who recommended the [Δm, n, 2 statistic](https://mol.ax/software/delta/). It looks very relevant for the case of two potential parent lineages. Still I did not find time...

To make it easier to distinguish real recombinants and sequencing artifacts, I want to add the most relevant primers to Sc2rf. Currently, this involves adding the `.bed` files to the...