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Adeschen patch 1 - #614

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adeschen wants to merge 738 commits into

KrasnitzLab:adeschen-patch-1from

adeschen:adeschen-patch-1

Closed

Adeschen patch 1#614
adeschen wants to merge 738 commits into
KrasnitzLab:adeschen-patch-1from
adeschen:adeschen-patch-1

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Commits on Sep 29, 2023
- Merge branch 'main' of https://github.com/belleau/RAIDS
  
  belleau
  authored and
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  committed
  ea30ff5
- Update the man for pathGeno
  
  belleau
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  87c1422
- Move genotypes CSV files to sub-directory in inst/extdata and adapt documentation accordingly
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  15f3a25
- Merge pull request #530 from belleau/main
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  184ff78
- Merge branch 'KrasnitzLab:main' into main
  adeschen
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  4b7fe78
- Merge pull request #531 from adeschen/main
  adeschen
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  efb03ee
- Cange extension of README file and update content
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  f6b0ea9
- Update the vignette with VCF
  
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  f95b316
- Update the vignette with VCF
  
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  20de296
- Merge pull request #532 from adeschen/main
  adeschen
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  249f1e5
- Update README
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  b50aa22
- Merge pull request #533 from belleau/main
  adeschen
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  63d3f49
- Merge pull request #534 from adeschen/main
  adeschen
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  8e225e5
- Update README
  adeschen
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  eb802e2
- Merge pull request #535 from adeschen/main
  adeschen
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  5827bd3
- Update README example
  
  belleau
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  8ab4c74
- Merge pull request #536 from belleau/main
  adeschen
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  a1dcc0f
- Correct indents in Reference GDS vignette
  adeschen
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  4c77f93
- Update text in main vignette
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  1550d50
- Merge pull request #537 from adeschen/main
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- Merge pull request #538 from adeschen/main
  adeschen
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  73f7a5a
- Update package version to 0.99.12
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  d5490e0
- Merge pull request #539 from adeschen/main
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  9d63453
- Add values to biocViews in DESCRIPTION
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  64de5fe
- Merge pull request #540 from adeschen/main
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  c51989d
- Update doc for addGeneBlockGDSRefAnnot() function
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  e11e68e
- Update doc for generateGeneBloc() function
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  82f9a00
Commits on Sep 30, 2023
- Merge pull request #541 from adeschen/main
  adeschen
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  501b100
- Update version to 0.99.13
  adeschen
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  3201329
- Merge pull request #542 from adeschen/main
  adeschen
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  1749bf7
Commits on Oct 5, 2023
- Adding author
  adeschen
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  7c6742b
- Merge branch 'main' of https://github.com/adeschen/RAIDS
  adeschen
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  85db64a
- Merge pull request #543 from adeschen/main
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  2763fce
Commits on Oct 6, 2023
- Update biocViews field to removed unwamted term
  adeschen
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  e7e545e
- Merge pull request #544 from adeschen/main
  adeschen
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  adab585
- Update package version to 0.99.14
  adeschen
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  b482829
- Merge pull request #545 from adeschen/main
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Commits on Oct 12, 2023
- Update README
  adeschen
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  9ddc78e
- Merge pull request #546 from adeschen/main
  adeschen
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  5f57b92
- Update readme file
  adeschen
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  498c1f6
- Merge pull request #547 from adeschen/main
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  cdbc2e7
- Update installation section in vignette
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  1345a5e
- Merge pull request #548 from adeschen/main
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  f074c92
Commits on Oct 13, 2023
- Update version to 0.99.15
  adeschen
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  36ebb6f
- Merge pull request #549 from adeschen/main
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  eff286a
Commits on Oct 24, 2023
- bump x.y.z version to even y prior to creation of RELEASE_3_18 branch
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  committed
  12ea1e7
- bump x.y.z version to odd y following creation of RELEASE_3_18 branch
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  e58671a
Commits on Apr 30, 2024
- bump x.y.z version to even y prior to creation of RELEASE_3_19 branch
  jwokaty
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  a9ec943
- bump x.y.z version to odd y following creation of RELEASE_3_19 branch
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  8c31b43
Commits on Aug 5, 2024
- We stop to use pedProfile rownames. We changed function addStudyGDSSample.
  
  belleau
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  belleau
  committed
  d135565
- Update check-bioc.yaml
  adeschen
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  4a87821
- Merge pull request #1 from adeschen/patch-1
  belleau
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Commits on Aug 16, 2024
- Add createAccuracyGraph() function; change itemize to describe in doc
  adeschen
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  38d46f1
- Update test to correct error
  adeschen
  committed
  f539afb
- Update to r 4.4 and bioc 3.19
  adeschen
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  23f9fa5
- Update biocViews section
  adeschen
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  4a66297
- Update action item to v4
  adeschen
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  aa1f9ab
- Update package version to 1.3.1
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  501ff81
Commits on Aug 17, 2024
- Merge pull request #550 from adeschen/main
  adeschen
  authored
  fad869a
Commits on Aug 19, 2024
- Merge branch 'KrasnitzLab:main' into main
  belleau
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  6374022
Commits on Aug 31, 2024
- Updata addStudyGDSSample in gdsWrapper_internal.R
  
  belleau
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  79712a4
- In generateMapSnvSel change read.csv2 to read.csv
  
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  930b62d
Commits on Sep 4, 2024
- Merge pull request #551 from belleau/main
  adeschen
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  37db9b6
Commits on Sep 5, 2024
- Update createAccuracyGraph() to show y lab values
  adeschen
  committed
  645f796
- Merge branch 'main' of https://github.com/adeschen/RAIDS
  adeschen
  committed
  b70d066
- Update action test-coverage
  adeschen
  committed
  72f70d9
- Merge pull request #552 from adeschen/main
  adeschen
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  1e18e87
Commits on Sep 9, 2024
- add function select1KGPopForSynthetic in synthetic.R
  
  belleau
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  6069e9c
Commits on Sep 10, 2024
- Add functions runDNAAncestryProfile and runRNAAncestryProfile
  
  belleau
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  committed
  dd5daa9
- Rename functions runDNAAncestryProfile to inferAncestry.Rd and runRNAAncestryProfile to inferAncestryGeneAware
  
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Commits on Sep 11, 2024
- Add computeAncestryFromSynthetic
  
  belleau
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  dd43808
- Add function profileAncestry
  
  belleau
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  d24b7cd
- Changed the man of profileAncestry
  
  belleau
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  3938d28
- Add function wrapperAncestry
  
  belleau
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  33ac4f2
- Update function inferAncestry and inferAncestryGeneAware
  
  belleau
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  98cc871
- Add function createAUROCGraph
  
  belleau
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  belleau
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  8f57ec6
- Merge pull request #553 from belleau/main
  adeschen
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  a656ac9
Commits on Oct 10, 2024
- Solve a variable problem in profileAncestry and add some comments
  
  belleau
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  5831d42
Commits on Oct 11, 2024
- Don't allow createStudy2GDS1KG when the gds exists.
  
  belleau
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  committed
  e515426
- Add a test for createStudy2GDS1KG.
  
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  5e45004
- Add the function getRefSuperPop
  
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  d33eb47
Commits on Oct 15, 2024
- Add the function identifyRelativeRef wrapper of identifyRelative
  
  belleau
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  2856a66
- Merge pull request #554 from belleau/main
  adeschen
  authored
  3fab12b
- Update check-bioc.yaml
  adeschen
  authored
  cf062dd
- Update check-bioc.yaml
  adeschen
  authored
  0a49b99
- Merge pull request #555 from adeschen/main
  adeschen
  authored
  20bfad8
- Update check-bioc.yaml
  adeschen
  authored
  d0178e6
- Update generatePhase1KG2GDS and add wrapper generatePhaseRef
  
  belleau
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  belleau
  committed
  7a0f03c
- Merge pull request #556 from belleau/main
  adeschen
  authored
  f09f373
- Merge branch 'KrasnitzLab:main' into main
  adeschen
  authored
  4073172
- Merge pull request #557 from adeschen/main
  adeschen
  authored
  ca39ffd
- Update main steps figure
  adeschen
  committed
  a5d072f
- Add function processBlockChr and correct some importFrom
  
  belleau
  authored and
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  committed
  b0e3eab
- Add function addGeneBlockRefAnnot wrapper of addGeneBlockGDSRefAnnot
  
  belleau
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  belleau
  committed
  79692f8
- Adding wrapper vignette
  adeschen
  committed
  b6c173d
- Merge pull request #558 from belleau/main
  adeschen
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  bb4fbde
- Merge branch 'KrasnitzLab:main' into main
  adeschen
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Commits on Oct 16, 2024
- Merge pull request #559 from adeschen/main
  adeschen
  authored
  540e3fb
- Warning in red about new functions available
  adeschen
  committed
  b82f880
- Merge branch 'main' of https://github.com/adeschen/RAIDS
  adeschen
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  2af94c5
- Merge branch 'KrasnitzLab:main' into main
  adeschen
  authored
  e92a07a
- Remove old image for main steps section
  adeschen
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  31cae4f
- Merge branch 'main' of https://github.com/adeschen/RAIDS
  adeschen
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  d3a2b96
- Merge pull request #560 from adeschen/main
  adeschen
  authored
  6256b60
- Merge branch 'KrasnitzLab:main' into main
  adeschen
  authored
  4008f4f
- Merge pull request #561 from adeschen/main
  adeschen
  authored
  5aeea96
- Update main vignette
  adeschen
  committed
  4762a5b
- Merge branch 'main' of https://github.com/adeschen/RAIDS
  adeschen
  committed
  e93f536
- Merge pull request #562 from adeschen/main
  adeschen
  authored
  b4a3551
- Update main vignette
  adeschen
  committed
  bc8ec34
- Merge pull request #563 from adeschen/main
  adeschen
  authored
  6bbb29a
- Update to parse the plink output for LD blocks.
  
  belleau
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  belleau
  committed
  18056f2
- Merge branch 'main' of https://github.com/belleau/RAIDS
  
  belleau
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  belleau
  committed
  841e6a9
- Correct example for addGDS1KGLDBlock
  
  belleau
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  committed
  6c88638
- Merge pull request #564 from belleau/main
  adeschen
  authored
  7bceec5
- Update Description
  
  belleau
  authored and
  belleau
  committed
  6667021
- Correct example for addGDS1KGLDBlock
  
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  bdbca27
- Merge branch 'main' of https://github.com/belleau/RAIDS
  
  belleau
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  committed
  7602b79
- Merge pull request #565 from belleau/main
  adeschen
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Commits on Oct 18, 2024
- Add a validation to addBlockFromDetFile.
  
  belleau
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  6c36cd5
- Merge branch 'main' of https://github.com/belleau/RAIDS
  
  belleau
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  c781997
Commits on Oct 21, 2024
- Update vignette
  adeschen
  committed
  4d63292
- Merge pull request #566 from adeschen/main
  adeschen
  authored
  081e2da
Commits on Oct 22, 2024
- Update function documentation and correct indents
  adeschen
  committed
  388d94d
- Update vignette
  adeschen
  committed
  5025818
- Merge pull request #567 from adeschen/main
  adeschen
  authored
  8f2ea94
- Merge branch 'KrasnitzLab:main' into main
  belleau
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  87b9718
- Merge pull request #568 from belleau/main
  adeschen
  authored
  9b64817
- Increase version
  
  belleau
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  committed
  1199983
- Merge branch 'main' of https://github.com/belleau/RAIDS
  
  belleau
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  committed
  46e8309
- Merge pull request #569 from belleau/main
  adeschen
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- Merge remote-tracking branch 'origin/main'
  
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Commits on Oct 29, 2024
- bump x.y.z version to even y prior to creation of RELEASE_3_20 branch
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  committed
  6b32a2c
- bump x.y.z version to odd y following creation of RELEASE_3_20 branch
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  committed
  bb243c9
Commits on Apr 9, 2025
- Update title in DESCRIPTION file
  adeschen
  committed
  7ba504a
- Merge pull request #570 from adeschen/main
  adeschen
  authored
  ce9c260
- Update vignette title
  adeschen
  committed
  00c1ba2
- Merge pull request #571 from adeschen/main
  adeschen
  authored
  cf9bc69
Commits on Apr 10, 2025
- Update check-bioc
  adeschen
  committed
  d7bdaea
- Merge pull request #572 from adeschen/main
  adeschen
  authored
  ba92d06
- Add function extractNucleotide and processPileupChrBin
  
  belleau
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  committed
  33e0327
- Merge branch 'main' of https://github.com/belleau/RAIDS
  
  belleau
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  belleau
  committed
  c47f0e4
- Update README
  adeschen
  committed
  f2ae83d
- Merge branch 'main' of https://github.com/adeschen/RAIDS
  adeschen
  committed
  5da36d0
- Merge pull request #573 from adeschen/main
  adeschen
  authored
  a5a1bf8
- Merge pull request #574 from belleau/main
  adeschen
  authored
  5145ad9
- Merge pull request #4 from KrasnitzLab/main
  adeschen
  authored
  204f21e
- Update doc for extractNucleotid() function
  adeschen
  committed
  b2d024a
- Correct extractNucleotide() function
  adeschen
  committed
  34eb2fe
- Merge pull request #575 from adeschen/main
  adeschen
  authored
  ec7902a
- Adding tests for extractNucleotide() function
  adeschen
  committed
  bf8e02b
Commits on Apr 11, 2025
- Merge pull request #576 from adeschen/main
  adeschen
  authored
  70620b9
- Add function readSNVBAM
  
  belleau
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  committed
  30c5997
- Merge branch 'main' of https://github.com/belleau/RAIDS
  
  belleau
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  committed
  4e774b0
- Merge pull request #577 from belleau/main
  adeschen
  authored
  5b03a90
- Update doc and format processPileupChrBin() function
  adeschen
  committed
  8cc8b65
- Update RAIDS.Rmd
  krasnitz
  authored
  5b04cad
- Merge pull request #578 from adeschen/main
  adeschen
  authored
  64aa87a
- Merge pull request #5 from KrasnitzLab/main
  adeschen
  authored
  e2ac16f
- Add unit test for processPileupChrBin() function
  adeschen
  committed
  26c72ca
- Merge branch 'main' of https://github.com/adeschen/RAIDS
  adeschen
  committed
  b698dd3
- Merge pull request #579 from adeschen/main
  adeschen
  authored
  fb60b8f
- Add function generateProfileGDS
  
  belleau
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  committed
  dd2ee04
- Merge branch 'main' of https://github.com/belleau/RAIDS
  
  belleau
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  belleau
  committed
  f91aa80
- Merge pull request #580 from belleau/main
  adeschen
  authored
  7391a7e
- Update example in doc for processPileupChrBin() function
  adeschen
  committed
  2d91898
- Merge branch 'main' of https://github.com/KrasnitzLab/RAIDS
  
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  1f22615
- Merge remote-tracking branch 'upstream/devel'
  
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  committed
  adf231f
- Update to version 1.5.1
  
  belleau
  authored and
  belleau
  committed
  f9c7db5
- Update RAIDS.Rmd
  krasnitz
  authored
  3c005df
- Merge pull request #582 from belleau/main
  adeschen
  authored
  8656930
- Merge pull request #581 from adeschen/main
  adeschen
  authored
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Commits on Apr 13, 2025
- Add function createProfile and adapted the rest
  
  belleau
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  committed
  9969cfc
- Merge branch 'main' of https://github.com/belleau/RAIDS
  
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  3623eb5
Commits on Apr 14, 2025
- Update vignette step 1
  adeschen
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- Merge pull request #583 from adeschen/main
  adeschen
  authored
  3dcb3fe
- Update vignette
  adeschen
  committed
  a130c66
- Merge pull request #584 from adeschen/main
  adeschen
  authored
  2c88c53
- Update vignette
  adeschen
  committed
  643a443
- Merge branch 'main' of https://github.com/adeschen/RAIDS
  adeschen
  committed
  db68d0e
- Merge pull request #586 from belleau/main
  adeschen
  authored
  ede1f3f
- Merge pull request #585 from adeschen/main
  adeschen
  authored
  2274812
- Tuning the functions for Rsamtools part 2
  
  belleau
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  committed
  2eb8e60
- Merge branch 'main' of https://github.com/belleau/RAIDS
  
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Commits on Apr 15, 2025
- Merge pull request #587 from belleau/main
  adeschen
  authored
  db5a712
- bump x.y.z version to even y prior to creation of RELEASE_3_21 branch
  jwokaty
  committed
  ed557dd
- bump x.y.z version to odd y following creation of RELEASE_3_21 branch
  jwokaty
  committed
  b3b3d8c
- Update RAIDS.Rmd
  krasnitz
  authored
  dc80748
- Update RAIDS.Rmd
  krasnitz
  authored
  b48574a
- Update RAIDS.Rmd
  krasnitz
  authored
  6fbfb87
- Update RAIDS.Rmd
  krasnitz
  authored
  575bee9
Commits on Apr 16, 2025
- Update RAIDS.Rmd
  belleau
  authored
  b4f6d1f
- Tuning the functions for Rsamtools part 3
  
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  committed
  3ab308b
- Merge branch 'main' of https://github.com/belleau/RAIDS
  
  belleau
  authored and
  belleau
  committed
  5e34f05
- Merge pull request #589 from belleau/main
  adeschen
  authored
  d17c99b
- Merge branch 'main' of https://github.com/belleau/RAIDS
  
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  authored and
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  committed
  c843799
- Update version
  
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  committed
  12305bb
- Merge remote-tracking branch 'origin/main'
  
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  authored and
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  committed
  c0dfd0f
- Merge pull request #590 from belleau/main
  adeschen
  authored
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Commits on May 1, 2025
- Update test-coverage.yaml
  adeschen
  authored
  a1c206b
- Merge pull request #8 from adeschen/adeschen-patch-5
  adeschen
  authored
  c6d83ba
- Merge pull request #593 from adeschen/main
  adeschen
  authored
  5614030
Commits on May 2, 2025
- Update README.md
  adeschen
  authored
  64dfaff
- Merge pull request #9 from adeschen/adeschen-patch-1
  adeschen
  authored
  eac329f
- Merge pull request #594 from adeschen/main
  adeschen
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Commits on May 6, 2025
Commits on May 7, 2025
- Merge pull request #598 from adeschen/main
  adeschen
  authored
  6c4531b
- Update createAccuracGraph() code and add unit tests
  adeschen
  committed
  2a9ecf8
- Merge pull request #599 from adeschen/main
  adeschen
  authored
  f9120e0
- Simplifying graph functions and adding unit tests
  adeschen
  committed
  6a6f5da
- Merge pull request #600 from adeschen/main
  adeschen
  authored
  0cf6904
- Add unit tess for readSNVFileGeneric() function
  adeschen
  committed
  09b7924
- Merge pull request #601 from adeschen/main
  adeschen
  authored
  e8afa57
Commits on May 8, 2025
- Adding unit test for readSNVVCF() function
  adeschen
  committed
  5ffb02c
- Update doc for readSNVVCF() and unit test
  adeschen
  committed
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- Merge pull request #602 from adeschen/main
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