Matthew J. Oldach

Varscan2 output ID column missing

1

I'm getting an [error trying to feed `Varscan2.3.9` data into `SnpEff`](https://github.com/pcingola/SnpEff/issues/267#issuecomment-736928876). The developer says this is because the `ID` column is missing.

ERROR:root:Unable to load cythonized quickconsensus module; this is likely because pysam has been updated since genomeview was originally install. To fix this, force reinstall genomeview: pip install --upgrade --force-reinstall genomeview

10

This is a follow up to #62 (which was on a shared academic HPC). I've now tried to download/run `svviz2` from Linux machine where I have root privileges. ``` sudo...

Add missing themes :art: :busts_in_silhouette:

1

There are **13 scales** however currently there are only **3 themes**. Generate a few more themes. Maybe also add a helper-function to make creating new themes + scales for PRs...

Where is output from training?

7

I've ran the following training script. There doesn't seem to be an obvious errors from the logs, so I think it ran successfully - just having trouble finding the output...

``` conda create -n cmr python=3 conda activate cmr conda install pytorch torchvision -c pytorch pip install -r requirements.txt ``` But I get many errors for almost all dependencies in...

How to get leaf indices that each sample was assigned to in the forest

2

In Python's `scikit-learn` the `ExtraTreesClassifier` function returns a numpy array which contains the leaf indices that each sample was assigned to in the forest. I'm trying to get similar information...

testRun failure

17

Trying to build RUFUS with gcc version ``` [moldach@cedar1 TOOL_TMP_DIR]$ wget https://github.com/jandrewrfarrell/RUFUS/archive/V1.0.tar.gz --2021-01-29 11:44:34-- https://github.com/jandrewrfarrell/RUFUS/archive/V1.0.tar.gz Resolving github.com (github.com)... 140.82.114.3 Connecting to github.com (github.com)|140.82.114.3|:443... connected. HTTP request sent, awaiting response... 302...

RUFUS creates incomplete VCF header

1

I've noticed the genotype in the `FORMAT` field is often `0/0, 0/0, 0/0` so there is likely some filtering I need to do. I was hoping to use `gatk VariantFiltration`...

There are some underlying functions in the Magic C++ library that have not yet been added to the R-wrapper {magick} yet: https://github.com/ropensci/magick/issues/316 Therefore it would be useful if this was...

django.db.utils.OperationalError: no such table: main.core_analysistype__old

19

I'm getting an error trying to install/run `genesysv`. After following the installation examples the following code is _partially_ working. I'm able to open but something in the error isn't loading...