Arnold Kuzniar

Add some info on automated C/C++ code review/analysis

2

for example, using Codacy (with [cppcheck](https://sourceforge.net/p/cppcheck/wiki/Home/)) or SonarQube (with [C++ plugin](http://github.com/wenns/sonar-cxx)). Anyone using these in the projects?

- [x] fix URL to (renamed) GH repo (#34) - [x] contact person changed to @c-martinez - [ ] add new project(s)?

Reason: We don't want to grant Docker Hub (almost) 'admin' privileges over all NLeSC repos.

Hi, Is there a compressor for floating point data implemented in the library? I would like to try NCD on a set of images. Thank you.

This concerns germline/somatic filtering steps (#11, #13) which are part of the SV calling rules of: - [ ] Manta - [ ] DELLY - [ ] LUMPY - [...

`bcftools` raises warnings: ``` [W::vcf_parse] Contig '1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '2' is not defined in the header. (Quick...

Update SV callers to the latest versions

2

- [ ] Manta v1.1.0 -> 1.6.0 - [ ] DELLY v0.7.7 -> 0.8.1 - [ ] LUMPY v0.2.13 -> 0.3.0 - [ ] GRIDSS v1.3.4 -> 2.7.3

Add rule(s): - [ ] `samtools faidx ...` - [ ] `bwa index ...`

Add an option to validate input e.g. using [Picard](https://broadinstitute.github.io/picard/command-line-overview.html#ValidateSamFile).