Clint Valentine

Tool to enable better visualization of basecall quality scores in sequencing data

1

Closes #58

Some thoughts: - [ ] New/removed `FORMAT` keys - [ ] New/removed `INFO` keys - [ ] Different VCF version - [ ] Updated header entry description - [ ]...

Sandbox PR.

```python import pandas as pd import matplotlib.pyplot as plt df = pd.read_csv("/Users/cvalentine/scratch/fastq-qual/1.csv") fig, ax = plt.subplots(figsize=(5, 10)) ax.imshow(df.values, aspect='auto') ```

These preferences each have a specific type associated with them, so constant object values are probably not the best way to store this data: https://github.com/clintval/cvbio/blob/b6965defbcb75cc9b73ac4e66e766f472c025e72/tools/src/com/cvbio/tools/igv/IgvPreferences.scala#L3-L39 All preferences defined here: https://github.com/igvteam/igv/blob/master/src/main/resources/org/broad/igv/prefs/preferences.tab

IGV renders responsive SVG, should we edit the resulting SVG and include a width and height in inches?

We have an older Dagr pipeline that has been run many times (updated to use 040d12e though). In very rare non-reproducible cases we appear to hit a deadlock that causes...

API should not allow mixins between VariableResources and FixedResources

3

The API allows you to mix in both `VariableResources` and `FixedResources` into the same task when I think the type checker or compiler should forbid the combination. For example, this...

Add a description of the toolkit to the README

2

Enhancing the README to better communicate how this toolkit works and should be used.