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 deletions.  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  pythonffi.cpp  for  the  existing  bindings  and  Variant.h  for the classes and
       accessors.

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