feat: Index for bam::IndexedReader

[tedil]

This PR addresses issue #386 by providing a struct IndexView analogous to HeaderView.

Since I'm not particularly well versed in interfacing with C and the htslib API, I'm a bit unsure if this is "the correct way" to handle this. There's no corresponding implementation for Clone yet, and I'm not sure what the point of the owned field of HeaderView is, since it does not seem to be modified anywhere.

This still needs some testcases, a simple one should be the one from the referenced issue.

[coveralls]

Pull Request Test Coverage Report for Build 4946873208

• 64 of 77 (83.12%) changed or added relevant lines in 1 file are covered.
• 3 unchanged lines in 2 files lost coverage.
• Overall coverage increased (+0.3%) to 79.293%

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Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
src/bam/mod.rs	64	77	83.12%

Files with Coverage Reduction	New Missed Lines	%
src/utils.rs	1	66.67%
src/bam/record.rs	2	76.33%

Totals
Change from base Build 4698271908:	0.3%
Covered Lines:	2332
Relevant Lines:	2941

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💛 - Coveralls

[tedil]

This currently only works for BAM + bai, not CRAM + crai, unsure why that is.

[tedil]

Ah, the cram index does not contain the necessary information, so the slow idxstats variant has to be used, see bam_index.c for more information

[tedil]

I've added an unpolished translation of the slow_idxstats method from samtools bam_index.c, which should be used in case of CRAM (and SAM) indexed files.

[johanneskoester]

Nice work! If I remember correctly, the owned flag was for destroying the header view, which is not always what you want. But I don't recall the details anymore and don't have the time to check the code. However, this one looks good to me for now.