Update some methods to accept Path input

[takutosato]

Description

This PR makes changes needed for supporting cloud input/output files in some Picard tools. (see broadinstitute/picard#1804)

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.

[takutosato]

@lbergelson could you take a look at my revised code? Thanks!