Remove reference_genome parameter from GenomicsDB constructor and refactor to move plink support to its own .h/.cc files

[nalinigans]

1. Reference Genome is not required for normal queries and is moved out of the constructor into methods - generate-vcf when broad-type gvcf files have to be created from GenomicsDB. Also, support for vcf header templates to be specified to generate-vcf has been added.
2. The plink support exposes a lot of internal classes that are not part of the release and breaks building Python/R bindings to GenomicsDB that are external to the project. Moved the support out of genomicsdb into its own header and implementation files - see genomicsdb_plink.h and genomicsdb_plink.cc.
3. Did some refactoring and cleanup of the code, but internal dependencies from plink need to be removed to allow for Python/R bindings. Also, the c unit test test_bgen.cc may need to be rewritten to use goodies from Catch2 and TempDir. Will probably have to give some thought to refactoring the bgen writer as this was mentioned in the gatk meeting. Will file Issues for these later.

[codecov]

Codecov Report

Merging #214 (977b373) into develop (5802023) will decrease coverage by 0.00%.
The diff coverage is 88.95%.

@@             Coverage Diff             @@
##           develop     #214      +/-   ##
===========================================
- Coverage    76.73%   76.72%   -0.01%     
===========================================
  Files          166      168       +2     
  Lines        25036    25027       -9     
  Branches       441      440       -1     
===========================================
- Hits         19212    19203       -9     
  Misses        5599     5599              
  Partials       225      225              

Impacted Files	Coverage Δ
tools/src/gt_mpi_gather.cc	69.65% <0.00%> (+0.44%)	⬆️
...nomicsdb/spark/api/GenomicsDBQueryInputFormat.java	69.04% <50.00%> (ø)
...in/java/org/genomicsdb/reader/GenomicsDBQuery.java	79.68% <75.00%> (ø)
src/main/cpp/src/api/genomicsdb_plink.cc	87.40% <87.40%> (ø)
src/main/cpp/include/api/genomicsdb_plink.h	93.25% <93.25%> (ø)
src/test/cpp/src/test_bgen.cc	80.51% <95.45%> (-6.99%)	⬇️
src/main/cpp/include/api/genomicsdb.h	90.26% <100.00%> (-1.97%)	⬇️
...c/main/cpp/include/config/genomicsdb_config_base.h	96.72% <100.00%> (+0.05%)	⬆️
src/main/cpp/src/api/genomicsdb.cc	93.50% <100.00%> (+3.76%)	⬆️
src/main/cpp/src/api/genomicsdb_field.cc	100.00% <100.00%> (ø)
... and 5 more

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[mlathara]

looks good