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[FEATURE] Multi-Layout file #209

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merged 3 commits into from
Jul 8, 2024
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@smehringer smehringer commented Jul 8, 2024

This PR adds the possibility of a a single Layout file featuring multiple layouts. This is important in case of a partitioned HIBF.

When reading a layout, we formerly read until the end of the file.
Now we read either until the end of the file is reached OR a new header starts.

To read all layouts out of a layout file, one need to iteratively call laout.read_from on the stream.

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vercel bot commented Jul 8, 2024

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Name Status Preview Updated (UTC)
hibf ✅ Ready (Inspect) Visit Preview Jul 8, 2024 5:34pm

@seqan-actions seqan-actions added the lint [INTERNAL] used for linting label Jul 8, 2024
@seqan-actions seqan-actions removed the lint [INTERNAL] used for linting label Jul 8, 2024
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codecov bot commented Jul 8, 2024

Codecov Report

Attention: Patch coverage is 0% with 1 line in your changes missing coverage. Please review.

Project coverage is 92.47%. Comparing base (b068f7e) to head (4fb5566).
Report is 64 commits behind head on main.

Current head 4fb5566 differs from pull request most recent head 9c02a5a

Please upload reports for the commit 9c02a5a to get more accurate results.

Files Patch % Lines
src/layout/layout.cpp 0.00% 0 Missing and 1 partial ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main     #209      +/-   ##
==========================================
- Coverage   99.94%   92.47%   -7.48%     
==========================================
  Files          45       46       +1     
  Lines        1820     1833      +13     
  Branches        0      570     +570     
==========================================
- Hits         1819     1695     -124     
- Misses          1        6       +5     
- Partials        0      132     +132     

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@smehringer smehringer requested a review from eseiler July 8, 2024 14:25
TEST(layout_test, read_from_partitioned_layout)
{
// layout consists of three partitions, written one after the other
std::stringstream ss{R"layout_file(#TOP_LEVEL_IBF fullest_technical_bin_idx:111
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Can you make something in the layout dependent on i (e.g. Some bin index), such that we can be sure that each layout is parsed?

@seqan-actions seqan-actions added lint [INTERNAL] used for linting and removed lint [INTERNAL] used for linting labels Jul 8, 2024
@smehringer smehringer requested a review from eseiler July 8, 2024 17:39
@eseiler eseiler merged commit 42e493f into seqan:main Jul 8, 2024
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3 participants