Kimmo Palin

Fixes a possible bug or changes function of cutN such that it will report all 'N' regions, including the ones at the beginning of sequence. Testing status: "works for me"

stats GC-depth calculation badly off for long reads

3

When calculating depth by GC content, samtools stats command ignores reads overlapping boundary between two GC bins. For short read data, it doesn't matter since, as explained in [stats.c](https://github.com/samtools/samtools/blob/651bf1469d1abd86a78b5e57c29b24a93598b0c3/stats.c#L1304) the...

Feature Request: Nested priors for common terms

7

Hi, I'm trying to play around with [sparse models](https://betanalpha.github.io/assets/case_studies/modeling_sparsity.html#35_Normal_Mixture_Population_Model) and would like to place `NormalMixture` prior with `Dirichlet` weights as the prior for the common terms. The code would be...

sites.vcf for chm13v2 (T2T) reference

5

Attached is a [sites.chm13v2.vcf.gz](https://github.com/brentp/somalier/files/9909071/sites.chm13v2.vcf.gz) file for chm13v2 reference which is approximately compatible with the provided sites files. It will likely provide 5 conflicts for following variants whose location is non...

Save a lot of time with large runs by not re-finding the adapters for every batch. Store the discovered adapters to a JSON file and load from there if the...

Hi, setting of the reference allele in the vcf fails (informatively, thank you for that) in almost all environments. The issue is at https://github.com/DecodeGenetics/popSTR/blob/3a5ca742116bee78490e8bbb6e2c47ffc7781334/msGenotyper.cpp#L549 A simple fix would be to...