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[FEATURE] binning_directory - #920

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smehringer merged 5 commits into
seqan:masterfrom
eseiler:feature/binning_directory
Feb 25, 2020
Merged

[FEATURE] binning_directory#920
smehringer merged 5 commits into
seqan:masterfrom
eseiler:feature/binning_directory

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@eseiler

@eseiler eseiler commented Apr 16, 2019

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Blocked by #933

Resolves #1562

TODO:

  • Snippets
  • Docs (grouping)
  • make parameters strong types
  • Debug streaming
  • Refactor tests

@eseiler
eseiler requested a review from smehringer April 16, 2019 14:49
@codecov

codecov Bot commented Apr 16, 2019

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Codecov Report

Merging #920 into master will increase coverage by 0.02%.
The diff coverage is n/a.

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #920      +/-   ##
==========================================
+ Coverage   97.63%   97.65%   +0.02%     
==========================================
  Files         235      236       +1     
  Lines        8908     9005      +97     
==========================================
+ Hits         8697     8794      +97     
  Misses        211      211              
Impacted Files Coverage Δ
...n3/search/dream_index/interleaved_bloom_filter.hpp 100.00% <0.00%> (ø)

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@eseiler
eseiler force-pushed the feature/binning_directory branch 2 times, most recently from f4c55c7 to b77dd42 Compare April 23, 2019 12:29
@eseiler
eseiler force-pushed the feature/binning_directory branch 3 times, most recently from 59fc34d to 9509b92 Compare May 7, 2019 13:41
@eseiler
eseiler force-pushed the feature/binning_directory branch 3 times, most recently from cb2762c to bbb625b Compare May 17, 2019 16:24
Comment thread include/seqan3/search/dream_index/binning_directory.hpp Outdated
Comment thread include/seqan3/search/dream_index/binning_directory.hpp Outdated
Comment thread include/seqan3/search/dream_index/binning_directory.hpp Outdated
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Comment thread include/seqan3/search/dream_index/detail/bitvector.hpp Outdated
Comment thread include/seqan3/search/dream_index/detail/bitvector.hpp Outdated
Comment thread include/seqan3/search/dream_index/detail/bitvector.hpp Outdated
Comment thread include/seqan3/search/dream_index/detail/bitvector.hpp Outdated
Comment thread include/seqan3/search/dream_index/detail/bitvector.hpp Outdated
@eseiler
eseiler force-pushed the feature/binning_directory branch 2 times, most recently from 004bc29 to 94885ed Compare June 20, 2019 13:30
@eseiler
eseiler requested a review from smehringer June 20, 2019 13:31
@eseiler
eseiler force-pushed the feature/binning_directory branch from 94885ed to 3c92278 Compare June 21, 2019 05:20

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Just some stuff I came across when scanning the code to evaluate if mitra can use it already.

Comment thread include/seqan3/search/dream_index/binning_directory.hpp Outdated
Comment thread include/seqan3/search/dream_index/detail/binning_directory_base.hpp Outdated
Comment thread test/unit/search/dream_index/binning_directory_test.cpp Outdated
@eseiler
eseiler force-pushed the feature/binning_directory branch from 3c92278 to 20fe7e5 Compare August 30, 2019 11:25
@marehr
marehr requested a review from smehringer September 30, 2019 15:01
@eseiler
eseiler removed the request for review from smehringer September 30, 2019 15:14
Comment thread include/seqan3/search/dream_index/binning_directory.hpp Outdated
Comment thread include/seqan3/search/dream_index/binning_directory.hpp Outdated
Comment thread include/seqan3/search/dream_index/binning_directory.hpp Outdated
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Comment thread include/seqan3/search/dream_index/detail/binning_directory_base.hpp Outdated
Comment thread test/performance/search/dream_index/binning_directory_benchmark.cpp Outdated
Comment thread test/performance/search/dream_index/binning_directory_benchmark.cpp Outdated
Comment thread test/performance/search/dream_index/binning_directory_benchmark.cpp Outdated
Comment thread test/unit/search/dream_index/binning_directory_test.cpp Outdated
Comment thread include/seqan3/search/dream_index/all.hpp Outdated
@eseiler
eseiler force-pushed the feature/binning_directory branch from 20fe7e5 to ab210b7 Compare January 24, 2020 06:53
@smehringer
smehringer requested a review from MitraDarja January 27, 2020 06:51

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Some minor things

Comment thread include/seqan3/search/dream_index/interleaved_bloom_filter.hpp Outdated
Comment thread include/seqan3/search/dream_index/interleaved_bloom_filter.hpp Outdated
Comment thread include/seqan3/search/dream_index/interleaved_bloom_filter.hpp Outdated
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Comment thread test/performance/search/dream_index/interleaved_bloom_filter_benchmark.cpp Outdated
Comment thread test/snippet/search/dream_index/interleaved_bloom_filter_get.cpp Outdated
Comment thread test/unit/search/dream_index/interleaved_bloom_filter_test.cpp
Comment thread include/seqan3/search/dream_index/interleaved_bloom_filter.hpp
Comment thread include/seqan3/search/dream_index/interleaved_bloom_filter.hpp
@eseiler
eseiler force-pushed the feature/binning_directory branch from 04fb9c4 to ba3680e Compare February 11, 2020 12:20
Comment thread include/seqan3/search/dream_index/interleaved_bloom_filter.hpp Outdated
Comment thread include/seqan3/search/dream_index/interleaved_bloom_filter.hpp
Comment thread include/seqan3/search/dream_index/interleaved_bloom_filter.hpp

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Looks goods, just some small things. :)

Comment thread include/seqan3/search/dream_index/interleaved_bloom_filter.hpp Outdated
Comment thread include/seqan3/search/dream_index/interleaved_bloom_filter.hpp Outdated
Comment thread include/seqan3/search/dream_index/interleaved_bloom_filter.hpp Outdated
@eseiler
eseiler requested a review from MitraDarja February 13, 2020 13:03

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Looks good to me. :)

Comment thread include/seqan3/search/dream_index/interleaved_bloom_filter.hpp Outdated
Comment thread include/seqan3/search/dream_index/interleaved_bloom_filter.hpp Outdated
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@eseiler
eseiler force-pushed the feature/binning_directory branch from 9156803 to 58223ca Compare February 19, 2020 09:13
@eseiler
eseiler requested a review from smehringer February 19, 2020 09:31
Comment thread test/include/seqan3/test/performance/sequence_generator.hpp Outdated

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only tiny 💅 and then we can check the hash function once I have some tests on the uniformity

Comment thread include/seqan3/search/dream_index/interleaved_bloom_filter.hpp Outdated
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Comment thread include/seqan3/search/dream_index/interleaved_bloom_filter.hpp
Comment thread include/seqan3/search/dream_index/interleaved_bloom_filter.hpp Outdated
@eseiler
eseiler requested a review from smehringer February 20, 2020 12:24
@eseiler eseiler mentioned this pull request Feb 21, 2020
eseiler added a commit to Clemapfel/seqan3 that referenced this pull request Feb 23, 2020
@eseiler
eseiler force-pushed the feature/binning_directory branch from 339c607 to d3c9167 Compare February 25, 2020 08:33
Comment thread include/seqan3/search/dream_index/interleaved_bloom_filter.hpp Outdated
Comment thread include/seqan3/search/dream_index/interleaved_bloom_filter.hpp Outdated
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Comment thread include/seqan3/search/dream_index/interleaved_bloom_filter.hpp Outdated
@eseiler
eseiler requested a review from smehringer February 25, 2020 11:04
@smehringer
smehringer merged commit 3b6738d into seqan:master Feb 25, 2020
@eseiler
eseiler deleted the feature/binning_directory branch May 3, 2020 21:10
@rrahn rrahn mentioned this pull request Oct 12, 2020
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[FEATURE] Add the interleaved bloom filter

4 participants