Prerequisites for upgrading to htsjdk 2.19.0+

[cmnbroad]

Based on a GATK test run using a locally built htsjdk, the following are prerequisites to upgrading to the next htsjdk release (post-2.19.0):

• Subclass BCFCodec for use when reading from GenomicsDB #5839
• Fix CountReads and CountReadsSpark tests. These are failing because they specify src/test/resources/org/broadinstitute/hellbender/tools/chr7_1_20.interval_list as an interval argument. Since there is now a tribble codec that handles that extension, the file is treated as a picard interval list and parsed by the codec, but the file is not in picard interval list format.
• A release of Disq upgraded to the new htsjdk version (due to CRAM changes - Container.offset renamed to Container.byteOffset)
• Fix failing SortSamSparkIntegration.testSortBAMsSharded tests. Under investigation.

[cmnbroad]

Update: it appears that SortSamSparkIntegration.testSortBAMsSharded fails locally for me even on master (when run from intellij or from gradle), so that issue appears to be unrelated to the htsjdk upgrade.