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[FEATURE] Make the HIBF constructible from a layout file. #50

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merged 5 commits into from
Aug 24, 2023

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@smehringer smehringer commented Aug 22, 2023

This is needed s.t. raptor can still have the submodule raptor layout.
We want to keep layouting and building separate s.t. it can be easily benchmarked independently. It counts as a preprocessing step.

Things discussed:

  • Should the ctor be called with a filename or a stream? Put differently: Should the user care for opening the file or the hibf lib? When supplying a stream the ctor is more flexible as the user could keep the file in memory instead of writing it to disk.
    [RESOLUTION: for now, only stream. Later on maybe both.]
  • How to integrate the HIBF lib with chopper: The HIBF lib can read a layout but needs the input_fn. Thus, the user has to make sure to provide the correct hash_function. Chopper could write an additional header that provides all the files in the correct order.
    [RESOLUTION: chopper will add more meta information at the start of the layout file that raptor can parse but the hibf lib will ignore]
    • How should the extra header in chopper look like? [RESOLUTION: Starts with @]
    • should the HIBF lib be able to read it or only raptor? [RESOLUTION: No]
    • what does the HIBF lib do with the chopper extra header if supplied? [RESOLUTION: ignore it]

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vercel bot commented Aug 22, 2023

The latest updates on your projects. Learn more about Vercel for Git ↗︎

Name Status Preview Comments Updated (UTC)
hibf ✅ Ready (Inspect) Visit Preview 💬 Add feedback Aug 23, 2023 0:00am

@seqan-actions seqan-actions added the lint [INTERNAL] used for linting label Aug 22, 2023
@seqan-actions seqan-actions removed the lint [INTERNAL] used for linting label Aug 22, 2023
@seqan-actions seqan-actions added the lint [INTERNAL] used for linting label Aug 22, 2023
@seqan-actions seqan-actions removed the lint [INTERNAL] used for linting label Aug 22, 2023
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codecov bot commented Aug 22, 2023

Codecov Report

Patch coverage: 100.00% and project coverage change: +0.76% 🎉

Comparison is base (6ccdaaf) 91.10% compared to head (a2fa58b) 91.87%.

Additional details and impacted files
@@            Coverage Diff             @@
##             main      #50      +/-   ##
==========================================
+ Coverage   91.10%   91.87%   +0.76%     
==========================================
  Files          37       40       +3     
  Lines        1226     1341     +115     
==========================================
+ Hits         1117     1232     +115     
  Misses        109      109              
Files Changed Coverage Δ
include/hibf/config.hpp 100.00% <ø> (ø)
...ude/hibf/hierarchical_interleaved_bloom_filter.hpp 89.65% <ø> (ø)
include/hibf/detail/layout/layout.hpp 93.54% <100.00%> (ø)
src/config.cpp 100.00% <100.00%> (ø)
src/detail/layout/layout.cpp 100.00% <100.00%> (ø)
src/hierarchical_interleaved_bloom_filter.cpp 80.95% <100.00%> (+2.28%) ⬆️

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@seqan-actions seqan-actions added the lint [INTERNAL] used for linting label Aug 23, 2023
@seqan-actions seqan-actions added lint [INTERNAL] used for linting and removed lint [INTERNAL] used for linting labels Aug 23, 2023
@seqan-actions seqan-actions removed the lint [INTERNAL] used for linting label Aug 23, 2023
@smehringer smehringer marked this pull request as ready for review August 23, 2023 11:59
@seqan-actions seqan-actions added lint [INTERNAL] used for linting and removed lint [INTERNAL] used for linting labels Aug 23, 2023
@seqan-actions seqan-actions added lint [INTERNAL] used for linting and removed lint [INTERNAL] used for linting labels Aug 23, 2023
@smehringer smehringer mentioned this pull request Aug 24, 2023
25 tasks
@eseiler eseiler merged commit 1e269ec into seqan:main Aug 24, 2023
26 checks passed
@smehringer smehringer deleted the from_layout branch August 29, 2023 06:43
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3 participants