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Alignment configuration free end gaps - #1938

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smehringer merged 4 commits into
seqan:masterfrom
smehringer:alignment_configuration_free_end_gaps
Jul 24, 2020
Merged

Alignment configuration free end gaps#1938
smehringer merged 4 commits into
seqan:masterfrom
smehringer:alignment_configuration_free_end_gaps

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@smehringer

@smehringer smehringer commented Jun 26, 2020

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Part of seqan/product_backlog#96

I split the tasks such that the PR doesn't become too large.

Fixes tasks 1 & 2:

  • Introduce strong types free_end_gaps_sequence[1/2]_[leading/trailing]
  • Make seqan3::method_global a pipeable ocnfig element (not a tag), that is constructible from the 4 strong_types

@smehringer
smehringer marked this pull request as draft June 26, 2020 14:28
@smehringer
smehringer force-pushed the alignment_configuration_free_end_gaps branch 2 times, most recently from 400f90f to 74f2fc8 Compare July 3, 2020 08:22
@codecov

codecov Bot commented Jul 3, 2020

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Codecov Report

Merging #1938 into master will increase coverage by 0.00%.
The diff coverage is 100.00%.

Impacted file tree graph

@@           Coverage Diff           @@
##           master    #1938   +/-   ##
=======================================
  Coverage   97.88%   97.89%           
=======================================
  Files         261      262    +1     
  Lines        9831     9865   +34     
=======================================
+ Hits         9623     9657   +34     
  Misses        208      208           
Impacted Files Coverage Δ
...qan3/alignment/pairwise/alignment_configurator.hpp 100.00% <ø> (ø)
...e/seqan3/alignment/pairwise/detail/type_traits.hpp 100.00% <ø> (ø)
...ring/detail/simd_match_mismatch_scoring_scheme.hpp 100.00% <ø> (ø)
...ment/scoring/detail/simd_matrix_scoring_scheme.hpp 100.00% <ø> (ø)
...n3/alignment/configuration/align_config_method.hpp 100.00% <100.00%> (ø)
include/seqan3/range/views/kmer_hash.hpp 100.00% <0.00%> (ø)
include/seqan3/range/views/minimiser_hash.hpp 100.00% <0.00%> (ø)
...ude/seqan3/range/detail/random_access_iterator.hpp 100.00% <0.00%> (ø)
...de/seqan3/range/container/bitcompressed_vector.hpp 100.00% <0.00%> (ø)
...n3/search/dream_index/interleaved_bloom_filter.hpp 100.00% <0.00%> (ø)
... and 4 more

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@smehringer
smehringer force-pushed the alignment_configuration_free_end_gaps branch from 74f2fc8 to eb9e225 Compare July 20, 2020 08:18
@smehringer
smehringer requested review from a team, Irallia and MitraDarja and removed request for a team and MitraDarja July 20, 2020 08:26
@smehringer
smehringer marked this pull request as ready for review July 20, 2020 09:16
@smehringer
smehringer force-pushed the alignment_configuration_free_end_gaps branch from eb9e225 to c1c7bcd Compare July 20, 2020 12:12

@Irallia Irallia left a comment

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LGFM, thank you!

@smehringer
smehringer requested a review from eseiler July 22, 2020 08:19

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This probably does affect users?
If so, add a changelog entry (except it was added after the last release).
BTW, we do not have [NOP] labels for commits :D

Comment thread include/seqan3/alignment/configuration/align_config_method.hpp
@smehringer

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This probably does affect users?
If so, add a changelog entry (except it was added after the last release).

I will add one with the last PR for free end gaps. since right now the change would say
make method_global to method_global{} but after the last PR it will be
make method_global | aligned_ends{free...} to method_global{free...}. I think the in between won't need to be mentioned?

Comment thread include/seqan3/alignment/configuration/align_config_method.hpp Outdated
@smehringer
smehringer requested a review from eseiler July 23, 2020 05:45
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eseiler commented Jul 23, 2020

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Do you want to rebase or should I squash?

@smehringer
smehringer force-pushed the alignment_configuration_free_end_gaps branch from 1a2171c to d58bebc Compare July 23, 2020 15:17
@smehringer
smehringer merged commit 09254ef into seqan:master Jul 24, 2020
@Irallia
Irallia requested review from eseiler and removed request for eseiler July 27, 2020 09:03
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3 participants