Add basic functionality to read indexed FASTA files #165
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dlaehnemann
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Jun 8, 2020
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@brainstorm requested a review, so here it comes. Let me know, if I should have another look.
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Dear @dlaehnemann, thank you very much for the review! |
brainstorm
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Aug 4, 2020
* Cherry pick the pull request for faidx #165 (review) * Cargo formatting * Update faidx documentation for clarification * Implement faidx_open test * Run actions on faidx branch * Remove faidx from github actions * Activate CI for faidx branch * update osx bindings with faidx support * update linux bindings for faidx * Drop faidx branch from CI actions As requested by @brainstorm (see #214 (comment)) * Migrate faidx to use thiserror instead of snafu (#214 (comment)) * Use i64 in faidx and return byte array Internal C method faidx_fetch_seq64 uses i64 as type to index into large FASTA sequences. The fetch function now returns a byte array instead of a String to be more efficient. A new method was added to automatically convert to a String for convenience. * Formatting using cargo fmt * Use usize-type for position paramter in faidx The return type of the faidx functions is changed to a Result capturing a potential failure in converting the usize into a i64 (hts_pos_t in the C API). * Correct typo in faidx-error: to -> too Co-authored-by: Patrick Marks <[email protected]> Co-authored-by: Patrick Marks <[email protected]> Co-authored-by: Roman Valls Guimera <[email protected]>
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Hi,
this pull request adds basic FAIDX functionality. Importantly, not all functions are supported/wrapped but enough for my use case.
I tried to follow your coding conventions but please don't hesitate to point out anything which can be improved.
Best,
Manuel