adding HLAscan as a new module

[chrstphdm]

Description of feature

Hello,

As described in #145, adding more typing tools could allow us (among other things) to set up a result combination algorithm. If you compare it to other, HLAscan do not offer the best results (according to this and this benchmark for exemple) but is easy to setup and dataset used should be updatable (from IMGT/HLA EMBL flat file and some awk magic powder).

Algorithm/tool short description

All HLA typing algorithms can be divided into two broad categories: methods that assemble small reads de novo into longer contigs, and methods that directly match reads to HLA reference sequences. HLAscan belongs to the second group. At least 4 fields resolution is expected for class I and II loci.

Original paper

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1671-3

Source code/binary

Source code is not available, only binaries : https://github.com/SyntekabioTools/HLAscan

Licence

HLAscan software is freely available for academic purposes and a license is required for commercial download and installation

[apeltzer]

Similar issue (saw also the discussion on Slack): Licencing and only binaries available 👎🏻 Epitopeprediction had similar issues, where eventually some open source method provided better rersults than the proprietary closed source thing and we "kind of dropped" it there (mhcpan / netmhcpan).