Mark Chen

`NaN` in computeMatrix

1

Hi there, thank you for developing deeptools. I have a question. I have a small number of `NaN` in the output file (`-o`) of `computeMatrix reference-point`. Where do they come...

Installing using brew on Mac OSX Sierra, I got the error: ``` ==> Installing mikessh/repseq/vdjtools dependency: r ==> Downloading https://homebrew.bintray.com/bottles/r-3.4.3_1.sierra.bottle.tar.gz ######################################################################## 100.0% ==> Pouring r-3.4.3_1.sierra.bottle.tar.gz Error: The `brew link` step...

fix: update gene symbol when it is `None` and `AssemblyMapper` normalizer

1

Two fixes: 1. The `_update_gene_symbol` of `VariantMapper` class did not update symbol when it is `None`. 2. The normalizer of `AssemblyMapper` uses a `VariantMapper` configured inconsistently from `AssemblyMapper` itself. The...

p type cannot be validated

1

**Describe the bug** I get an error message of `AttributeError: 'AARefAlt' object has no attribute 'ref_n'` when using `validate()` against a protein variant. **To Reproduce** Steps to reproduce the behavior,...

Where iMHC scores are stored in the data model?

2

Hi there, thanks for developing CONGA! I wonder where the iMHC scores are stored in the data model or individual output file(s). Thanks! -Mark

Use modules or not

1

Hi there, I have a general question if I should modules or not for my project. I was re-directed from the [blog post](https://www.nextflow.io/blog/2019/one-more-step-towards-modules.html). I like the code in the module...