Subclass BCFCodec for use when reading from GenomicsDB

[cmnbroad]

The BCFCodec in the next release of htsjdk (after 2.19) will reject any BCF input that is greater than BCF 2.1 (see #5838 and samtools/htsjdk#1323). However, GenomicsDB uses htslib, which generates version 2.2 output, to create BCF streams for GATK (with the BCF IDX fields removed). This will no longer work with post-2.19 htsjdk versions.

Since GATK bypasses codec discovery and provides the codec directly for GenomicsDB inputs, the proposed solution is to change to the BCF codec in htsjdk to delegate version checking to an overridable method(!), and then provide a subclassed codec in GATK that has relaxed version checking.

[cmnbroad]

The htsjdk branch for this is here and the GATK branch is here. We'll need this for the next (post 2.19) htsjdk update. Will require the htsjdk branch to be merged and released before we can use the GATK branch.

[cmnbroad]

Done long ago #6305.