jackkamm

https://github.com/dengste/org-caldav/pull/294 converted the Readme to an Info manual, and did some re-organization, but there are still some improvements to be made both in content and formatting. For example: 1. Add...

After installing termite with this script, I get the following error when trying to run `xfce4-terminal`: ``` jack@jaheira:~/software/termite-install (git)-[master]- % xfce4-terminal xfce4-terminal: symbol lookup error: xfce4-terminal: undefined symbol: vte_terminal_set_bold_is_bright ```

Handle markers properly

3

PR https://github.com/jackkamm/undo-propose-el/pull/21 by @takaxp fixes a problem with `org-clock-marker`, but this problem is a symptom of a deeper problem, that we don't currently handle markers in the undo-propose buffers. ###...

Ruby tests breaking

3

When I tried to run the unit tests today, the ruby tests all broke with errors like: ``` (ert-test-failed ((should (progn (org-babel-execute-src-block) (sleep-for 0 400) (string= ... ...))) :form (progn...

[minor] Better handling of skipping ERCC process

2

The `quantifyERCCs` step should only happen when doing MSSPE sequencing, not ARTIC sequencing. Currently, we de facto skip it for ARTIC -- in particular, we still run the process, but...

[meta] Pipeline and repo cleanup

1

The current pipeline has a bit of bloat with processes we generally don't use: - `quast` - `multiqc` Remove these processes since we aren't using them. Also, this repo has...

Unpaired reads and bad test sample

1

While getting single-end reads working, I noticed a strange behavior with the test sample `RR057e_00734_subsampled`. It seems like there's an issue with the mate pairing for this test sample. When...

Currently, if >=10% of reads contain an insertion, but fewer than 90% have it, our pipeline will insert an N into the final sequence, possibly causing a frameshift. Our preference...

Both of these tests currently result in 0 reads aligning to the reference genome. For the case of test_fasta_reads, all aligning reads are removed by ivar trim for missing quality...

Fixes #150 This seems to be working, but I plan to add some unit tests before merging. Also should update the documentation to note this is supported now, but only...