Ricky Magner
Ricky Magner
Hi, I tried running some tools on an output VCF from PEPPER, and ran into a nonstandard base, which caused a lot of tools to throw an error. The problem...
[BUG] None value assignment in structs not handled properly causing indefinite hanging in terminal
This is a bug report that seems to be caused by the `None` type introduced in version 1.1 not being handled properly when assigned to fields in custom structs. Consider...
### Description of the issue: For "multiallelic" sites containing a spanning deletion alleles (represented by `*`), the `getType` method in `VariantContext` behaves somewhat unexpectedly. There have been numerous old discussions...
### Description of the issue: When using the `SAMFileWriterFactory` to write a .`cram` file, when the "create index" default is toggled on, it will create a `.bai` file for the...
### Description of the issue: Using the Histogram methods to get values when the histogram is empty are implemented in an unsafe way, leading to unhelpful error messages in some...
Hi, Both the provided `Dockerfile` and `Dockerfile.centos6` fail to build for me. The first results in the following error: ``` => [ 9/15] RUN wget http://archive.apache.org/dist/ant/binaries/apache-ant-1.9.7-bin.tar.gz && tar xzf apache-ant-1.9.7-bin.tar.gz...
Hi, this issue concerns `bcftools annotate` and its optional header `-h` input. I'll demonstrate with an example below (all run with v1.18). Suppose you have the following `test.vcf`: ``` ##fileformat=VCFv4.3...
## Bug Report ### Affected tool(s) or class(es) SelectVariants ### Affected version(s) - [x] Latest public release version [4.5.0.0] ### Description When trying to stream a reference file from a...
**Describe your context** Please provide us your environment, so we can easily reproduce the issue. - replace the result of `pip list | grep dash` below ``` dash 2.16.1 dash-core-components...
Hi, I opened [this question](https://www.biostars.org/p/9590235/) on Biostars over a week ago, and was wondering if anyone here might have an answer. Currently, the documentation in the main README isn't clear...