cvbio

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Add the scaffold of an ALT alignment post-processor

1

clintval

cvbio runs into error with recent openjdk version

1

When I installed cvbio v3.0.0 via bioconda, without specifying openjdk version, it installed successfuly with openjdk v17.0.3. However when executed, cvbio ran into this error: ``` Unrecognized VM option 'AggressiveOpts'...

ManavalanG

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

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Closes #58

clintval

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

clintval

Sandbox PR.

clintval

```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') ```

clintval

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

clintval

clintval

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

clintval