VCFLib Python FFI

       We  are building up a Python FFI for vcflib using the brilliant Python pybind11 module.  Mostly for (our)
       testing purposes, so we are not aiming for complete coverage.  See below for adding new bindings.

   Setting it up and example
       First  import  the  module.   It  may  require   setting   the   PYTHONPATH   to   the   shared   library
       pyvcflib.cpython-39-x86_64-linux-gnu.so.

              env PYTHONPATH=./build python3 -c 'import pyvcflib'

       in a GNU Guix shell you may prepend LD_LIBRARY_PATH to find GLIBC etc.

              LD_LIBRARY_PATH=$LIBRARY_PATH

       Now  you  should  be able to use the pyvcflib module.  Let’s try with a VCF samples/10158243.vcf that has
       only one record:

              >>> from pyvcflib import *

              >>> vcf = VariantCallFile()
              >>> vcf.openFile("../samples/10158243.vcf")
              True

              # ...    list(rec.name,rec.pos,rec.ref,rec.alt)

              >>> rec = Variant(vcf)
              >>> while (vcf.getNextVariant(rec)):
              ...    [rec.name,rec.pos,rec.ref]
              ['grch38#chr4', 10158243, 'ACCCCCACCCCCACC']

              >>> rec.alt[0]
              'ACC'

              >>> rec.alleles
              ['ACCCCCACCCCCACC', 'ACC', 'AC', 'ACCCCCACCCCCAC', 'ACCCCCACC', 'ACA']

       So the one input record shows it has a ref of `ACCCCCACCCCCACC' and six alt  alleles  [`ACCCCCACCCCCACC',
       `ACC', `AC', `ACCCCCACCCCCAC', `ACCCCCACC', `ACA'].

       This works fine!

   Masking genotypes
       With  vcfwave’s  allelic primitives, when two VCF records get combined, we need to combine the genotypes.
       This happens, for example, with vcfwave deletions.

       When a deletion spans any SNPs from realignment we want to make sure the SNPs are masked for those  dele‐
       tions.  I.e.

              6/28/2022, 4:21:44 PM - erikg:
              if you have a deletion in hap 1
                      .|0 or .|1
              in hap 2
                      0|. or 1|.
              etc.

       So,  if we have input two variants at the same position with the first a DEL and the second a SNP the SNP
       genotypes need to be masked as

              >> deletion_mask_genotypes(['1|0', '0|0', '0|1', '1|1', '1|0', '1|0', '1|1'],
              ...                         ['0|0', '1|1', '1|0', '0|0', '1|0', '1|1', '1|1'])
                                          ['0|0', '1|1', '1|0', '0|0', '.|0', '.|1', '.|.']

       In the 5-7th column the deletion has the same genotype and gets masked.

   Another example
       See realign.py for examples of using the FFI in the form of a python unit test.  We used that to  develop
       the vcfwave module.

   Additional bindings
       It  may  be  the  case you want additional bindings that we have not included yet.  See vcflib’s pythonf‐
       fi.cpp for the existing bindings and Variant.h for the classes and accessors.

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