Update to Hadoop-BAM 7.8.0

[fnothaft]

Bumps to latest version of HTSJDK. Should tack on to #1440. Will need to update SAM/BAM/CRAM queryname sorted loading code. As part of that fix, we should consolidate the BAM->Fragments path into a loadBamAsFragments method, which will make it easier to use downstream (e.g., in https://github.com/heuermh/cannoli/pull/15).

[heuermh]

While we're in there I'd suggest taking out

} else if (filePath.endsWith(".reads.adam")) {
  log.info(s"Loading $filePath as ADAM AlignmentRecords and converting to Fragments.")
  loadAlignments(filePath).toFragments

And from loadAlignments

} else if (filePath.endsWith("contig.adam")) {
  log.info(s"Loading $filePath as Parquet of NucleotideContigFragment and converting to AlignmentRecords. Projection is ignored.")
  AlignmentRecordRDD.unaligned(loadParquetContigFragments(filePath).toReads)

Sorry, I'll create a new issue. See #1456.