This refactor a bit the BAM Reader interface to accept an already open index. I had some code where opening the index was the bottleneck, I could probably have rewritten it a bit to avoid creating several Readers but it's still good to support that case I think.
Types of changes
This PR implements the following changes:
(Please tick any or all of the following that are applicable)
[x] :sparkles: New feature (A non-breaking change which adds functionality).
[ ] :bug: Bug fix (A non-breaking change, which fixes an issue).
[ ] :boom: Breaking change (fix or feature that would cause existing functionality to change).
:ballot_box_with_check: Checklist
[x] :art: The changes implemented is consistent with the julia style guide.
[x] :blue_book: I have updated and added relevant docstrings, in a manner consistent with the documentation styleguide.
[ ] :blue_book: I have added or updated relevant user and developer manuals/documentation in docs/src/.
[x] :ok: There are unit tests that cover the code changes I have made.
[x] :ok: The unit tests cover my code changes AND they pass.
[ ] :pencil: I have added an entry to the [UNRELEASED] section of the manually curated CHANGELOG.md file for this repository.
[x] :ok: All changes should be compatible with the latest stable version of Julia.
[ ] :thought_balloon: I have commented liberally for any complex pieces of internal code.
This refactor a bit the BAM Reader interface to accept an already open index. I had some code where opening the index was the bottleneck, I could probably have rewritten it a bit to avoid creating several Readers but it's still good to support that case I think.
Types of changes
This PR implements the following changes: (Please tick any or all of the following that are applicable)
:ballot_box_with_check: Checklist
docs/src/.[UNRELEASED]section of the manually curatedCHANGELOG.mdfile for this repository.