Fix existing deprecations in code and build.

[tfenne]

Description

The build emits a number of Java deprecation warnings and gradle warnings about use of features incompatible with future gradle versions. This small PR fixes both.

Things to think about before submitting:

• Make sure your changes compile and new tests pass locally.
• Add new tests or update existing ones:
  • A bug fix should include a test that previously would have failed and passes now.
  • New features should come with new tests that exercise and validate the new functionality.
• Extended the README / documentation, if necessary
• Check your code style.
• Write a clear commit title and message
  • The commit message should describe what changed and is targeted at htsjdk developers
  • Breaking changes should be mentioned in the commit message.

[nh13]

LGTM