feat: Add rust_htslib::bcf::index::build

[PB-DB]

Builds a bcf/vcf index using the htslib bindings. It was useful to us, so I'm happy to share.

It's modeled after the equivalent in rust_htslib::bam::index. I've used it myself to verify behavior, but I haven't built any doc or unit tests.

Hope it's helpful!

Best,

Daniel

[johanneskoester]

Thanks!

[johanneskoester]

Can you please add a test case?

[PB-DB]

Sure!

I added some basic tests for successful construction from bcf + vcf.gz, as well as assert errors on building the wrong index format.

It would be convenient if it automatically chose 14 for a min shift for CSI files, or if we autodetected the index type to build, but I'm not sure it would make sense for the library. I'm happy to if you think it's worth it.

Thanks for building such a great resource!

[johanneskoester]

Sure!

I added some basic tests for successful construction from bcf + vcf.gz, as well as assert errors on building the wrong index format.

It would be convenient if it automatically chose 14 for a min shift for CSI files, or if we autodetected the index type to build, but I'm not sure it would make sense for the library. I'm happy to if you think it's worth it.

Thanks for building such a great resource!

Sure, feel free to extend the functionality in that direction in a follow-up PR! And thanks for liking rust-htslib!

[coveralls]

Pull Request Test Coverage Report for Build 7822478621

Details

• -10 of 33 (69.7%) changed or added relevant lines in 1 file are covered.
• 1 unchanged line in 1 file lost coverage.
• Overall coverage decreased (-0.1%) to 79.683%

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Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
src/bcf/index.rs	23	33	69.7%

Files with Coverage Reduction	New Missed Lines	%
src/bam/record.rs	1	76.72%

Totals
Change from base Build 7814288779:	-0.1%
Covered Lines:	2463
Relevant Lines:	3091

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💛 - Coveralls

[johanneskoester]

May I ask you to update to merge in the latest upstream master branch? It contains fixes for the failing tests.

[PB-DB]

Done - and thanks for figuring that out. Hope this fixes the tests! 🤞