Added alignment type to RecordAndOffset class

michaelgatzen commented 5 years ago

as requested per Picard pull request https://github.com/broadinstitute/picard/pull/1370
necessary to determine whether a RecordAndOffset object is an (alignment) match, insertion, or deletion when queried by a SamLocusIterator
default behavior is preserved by overloading the default constructor

Please explain the changes you made here. Explain the motivation for making this change. What existing problem does the pull request solve?

[ ] 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.

michaelgatzen commented 5 years ago

@lbergelson Agreed, I added lots of asserts in SamLocusIteratorTest. Also changed the description of the PR.

lbergelson commented 5 years ago

@michaelgatzen Thank you and congrats on your first htsjdk pr :)

samtools / htsjdk