Fixing argument namespace issue introduced with hguturu:hg-fix-pre-convert-gvcf

[nate-d-olson]

Fixing issue with args.convert_gvcf_truth missing from namespace in verion 0.3.13, described in #113 (comment).

To fix the issue I added --convert-gvcf-truth and --convert-gvcf-query arguments to hap.py.
Potential issue with hap.py having both --convert-to-vcf and --convert-gvcf-[truth|query].
Added conditional statement and defining new variables convert_gvcf_truth and convert_gvcf_query so that the gvcf to vcf conversion is performed if either convert_gvcf_to_vcf or convert_gvcf_[truth|query] flags are used.

Please merge this pull request, or another fix, and release a new version for snakemake/snakemake-wrappers#294.

[nate-d-olson]

Can we get this merged and released, or another kind of fix for this issue, please? Fixing this is a priority for the GIAB project.

[dskola]

Seems reasonable