Thomas Cokelaer

@iPsych not now but if you have a prototype, or are willing to add a PR, I'll be more than happy to incorporate it in the package with your contributions...

possible help with this code: http://sbml.org/Software/libSBML/5.17.0/docs//python-api/convert_s_b_m_l_8py-example.html

Dear @ntung I've just added you to the project. The project was on standby for a while but is now active again so welcome to the group !

at some point we should define precisely what BED means. We have some BED with 3,6,12 columns. Here, the BED file has 3 columns. What are the second and third...

using vcftools 0.1.14 , we can use this command: ``` vcftools --vcf test_vcf2bcf_v1.vcf --plink --out test.plink ``` This creates 2 filles though, a ped and a map file

information on - https://github.com/peterjc/maf2sam - https://raw.githubusercontent.com/arq5x/nanopore-scripts/master/maf-convert.py both are in Python2 format, first one relies on biopython, second one is pure python but seems to be SAM2MAF (not the inverse)

Thanks to the transitive framework, this works using MAF2SAM and SAM2BAM.

I will check out this issue. Just need to push à commit.

should be fix

Done with documentation, test and code