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Complete greedyMix features #24

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2 of 4 tasks
wleoncio opened this issue Jul 19, 2022 · 2 comments
Open
2 of 4 tasks

Complete greedyMix features #24

wleoncio opened this issue Jul 19, 2022 · 2 comments
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enhancement New feature or request

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@wleoncio
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wleoncio commented Jul 19, 2022 •
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The function currently loads the raw data, but doesn't process it. Check the code in greedyPopMix() and the original MATLAB code to see what else needs to be done (e.g. call handleData()).

To close the issue, make sure greedyMix() works for the following formats:

  • BAPS (test case)
  •  VCF
  •  BAM
  •  GenePop
@wleoncio wleoncio added the enhancement New feature or request label Jul 19, 2022
@wleoncio wleoncio self-assigned this Jul 19, 2022
wleoncio added a commit that referenced this issue Apr 8, 2024
@wleoncio
Fixed calculation of ninds ekat (#24)
f361975
wleoncio added a commit that referenced this issue Apr 8, 2024
@wleoncio
Improved handling of BAPS format (#24)
26ab010
wleoncio added a commit that referenced this issue Apr 8, 2024
@wleoncio
Bugfixes to indMix() and subfunctions (#24)
5c35b9a
wleoncio added a commit that referenced this issue Apr 8, 2024
@wleoncio
Fixed calculation og ninds (#24)
6c3e2af
wleoncio added a commit that referenced this issue Apr 8, 2024
@wleoncio
Fails for FAST input to greedyMix() (#24)
6209bb3 
This is a desirable feature, but was not implemented in the original BAPS, so better leave it out until the original planned features is working.
wleoncio added a commit that referenced this issue Apr 8, 2024
@wleoncio
Updated documentation (#24)
f676042
wleoncio added a commit that referenced this issue Apr 8, 2024
@wleoncio
Skips greedyMix() example until #24 is fixed
f5c0909
wleoncio added a commit that referenced this issue Apr 8, 2024
@wleoncio
Merge branch 'baps-format' into develop
9b8da3a 
* baps-format:
  Increment version number to 0.0.0.9025
  Skips `greedyMix()` example until #24 is fixed
  Updated documentation (#24)
  Fails for FAST input to `greedyMix()` (#24)
  Fixed calculation og `ninds` (#24)
  Bugfixes to `indMix()` and subfunctions (#24)
  Improved handling of BAPS format (#24)
  Fixed calculation of `ninds` `ekat` (#24)
  Added processing of BAPS format
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Implemented rest of algo, which got us back to the issue of an endless loop. Investigating indMix(), closely comparing its output with the one on the original BAPS...

wleoncio added a commit that referenced this issue Apr 11, 2024
@wleoncio
Added/renamed BAPS example data (#24)
98b5e7a
wleoncio added a commit that referenced this issue Apr 11, 2024
@wleoncio
Retranslated computePopulationLogml() (#24)
55d302a
wleoncio added a commit that referenced this issue Apr 11, 2024
@wleoncio
Using a dedicated environment for globals (#24)
5deadcf 
Based on suggestion from <https://stackoverflow.com/a/12605694/1169233>.
wleoncio added a commit that referenced this issue Apr 11, 2024
@wleoncio
laskeMuutokset() reads npop from parent functions (#24)
58a5e5a
wleoncio added a commit that referenced this issue Apr 11, 2024
@wleoncio
Changed default npops to 3 (#24)
c3b8da0
wleoncio added a commit that referenced this issue Apr 11, 2024
@wleoncio
Retranslated computeDiffInCounts() (#24)
55a36e8
wleoncio added a commit that referenced this issue Apr 11, 2024
@wleoncio
Syntax fix to indMix() (#24)
d1e567c
wleoncio added a commit that referenced this issue Apr 11, 2024
@wleoncio
Fixes to laskeMuutokset() (#24)
ec959fc
wleoncio added a commit that referenced this issue Apr 11, 2024
@wleoncio
Renamed global environment, fixed assignments (#24)
99f28ba
wleoncio added a commit that referenced this issue Apr 11, 2024
@wleoncio
Added (commented) test for BAPS data (#24)
2a815f1
wleoncio added a commit that referenced this issue Apr 11, 2024
@wleoncio
Merge branch 'issue-24' into develop
2d5d93a 
* issue-24:
  Increment version number to 0.0.0.9026
  Added (commented) test for BAPS data (#24)
  Renamed global environment, fixed assignments (#24)
  Fixes to `laskeMuutokset()` (#24)
  Syntax fix to `indMix()` (#24)
  Retranslated `computeDiffInCounts()` (#24)
  Changed default `npops` to 3 (#24)
  `laskeMuutokset()` reads `npop` from parent functions (#24)
  Using a dedicated environment for globals (#24)
  Retranslated `computePopulationLogml()` (#24)
  Added/renamed BAPS example data (#24)
wleoncio added a commit that referenced this issue Jul 2, 2024
@wleoncio
Fixed tests (#24)
e4af251
wleoncio added a commit that referenced this issue Jul 2, 2024
@wleoncio
Fixed indMix() and subfunctions (#24)
6aecf38
wleoncio added a commit that referenced this issue Jul 2, 2024
@wleoncio
Fixed greedyMix() for BAPS files (#24) 🍾
e873075
wleoncio added a commit that referenced this issue Jul 2, 2024
@wleoncio
Added unit tests (#24)
95ff237
wleoncio added a commit that referenced this issue Jul 2, 2024
@wleoncio
Merge branch 'issue-24' into develop
5cc111f 
* issue-24:
  Increment version number to 0.0.0.9028
  Updated docs
  Added unit tests (#24)
  Fixed `greedyMix()` for BAPS files (#24) 🍾
  Fixed `indMix()` and subfunctions (#24)
  Fixed tests (#24)
wleoncio added a commit that referenced this issue Aug 26, 2024
@wleoncio
Unwrapped `greedyMix() example (#24)
6e08c35
wleoncio added a commit that referenced this issue Aug 26, 2024
@wleoncio
Added function to convert from FASTA to BAPS (#24)
7b7968f
wleoncio added a commit that referenced this issue Aug 26, 2024
@wleoncio
Improved handling of FASTA data (#24)
ca358ff
wleoncio added a commit that referenced this issue Aug 26, 2024
@wleoncio
Improved conversion from FASTA to BAPS (#24)
471c380
wleoncio added a commit that referenced this issue Aug 26, 2024
@wleoncio
Adapted tests to FASTA on greedyMix() (#24)
b7282d6
wleoncio added a commit that referenced this issue Aug 26, 2024
@wleoncio
Ensure diffInCounts returns as.matrix (#24)
99e272a
wleoncio added a commit that referenced this issue Aug 26, 2024
@wleoncio
Added synthetic FASTA file (#24)
6f70f6f
wleoncio added a commit that referenced this issue Aug 26, 2024
@wleoncio
Disabled FASTA tests on greedyMix() (#24)
9ff5f39
wleoncio added a commit that referenced this issue Aug 26, 2024
@wleoncio
Merge branch 'issue-24' into develop
010f18d 
* issue-24:
  Increment version number to 0.0.0.9029
  Disabled FASTA tests on greedyMix() (#24)
  Added synthetic FASTA file (#24)
  Ensure diffInCounts returns as.matrix (#24)
  Adapted tests to FASTA on greedyMix() (#24)
  Removed baps file pointing to fasta
  Improved conversion from FASTA to BAPS (#24)
  Improved handling of FASTA data (#24)
  `process_BAPS_data()` can handle file being an R object
  Added function to convert from FASTA to BAPS (#24)
  Unwrapped `greedyMix() example (#24)
wleoncio added a commit that referenced this issue Sep 13, 2024
@wleoncio
Added GenePop data, txt and gen (#24)
12884cf
wleoncio added a commit that referenced this issue Sep 13, 2024
@wleoncio
Added unit tests for greedyMix() on GenePop (#24)
54b0b08
wleoncio added a commit that referenced this issue Sep 13, 2024
@wleoncio
Merge branch 'issue-24' into develop
1d87be9 
* issue-24:
  Updated docs
  Temp-wrapping disfunctional code
  Aligned processing of Genepop with MATLAB code
  Dropped support for GenePop on `importFile()`
  Added `process_GenePop_data()`
  Fixed `addAlleles()`
  handleData defaults to BAPS format
  Added unit tests for `greedyMix()` on GenePop (#24)
  Added GenePop data, txt and gen (#24)
wleoncio added a commit that referenced this issue Sep 27, 2024
@wleoncio
Added logml tests for #24
b57bc3f
wleoncio added a commit that referenced this issue Sep 27, 2024
@wleoncio
Updated NEWS.md (#24)
a3b65da
wleoncio added a commit that referenced this issue Sep 27, 2024
@wleoncio
Merge branch 'issue-24' into develop
8e51878 
* issue-24:
  Updated NEWS.md (#24)
  Increment version number to 0.0.0.9030
  Added logml tests for #24
  Fixed calculation of distances
  Fixed calculation of logml
  Adjusted unit tests
  Fixed output
  Syntax fixes
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Done for all originally-supported formats, namely BAPS and GenePop. VCF and BAM are not on the original code, so one needs to reshape them into a format the rest of the function can use. For FASTA, a function was created to convert it to BAPS. It's still broken, but might be the easiest way to go here.

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