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Development - #71

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alex-sandercock wants to merge 45 commits into

mainfrom

development

Open

Development#71
alex-sandercock wants to merge 45 commits into
mainfrom
development

Commits on Apr 22, 2026
- Merge pull request #58 from Breeding-Insight/development
  josuechinchilla
  authored
  f590dad
- corrected importFrom statement in parentage functions and ped_check
  
  josue.chinchilla
  authored and
  josue.chinchilla
  committed
  20d2764
- updated NAMESPACE to reflect updated importFrom statements
  
  josue.chinchilla
  authored and
  josue.chinchilla
  committed
  f2d3f40
- Update R/check_ped.R
  
  josuechinchilla
  and
  Copilot
  authored
  c1fe543
Commits on Apr 24, 2026
- updated error handling and reporting for check_ped, Also major improvement for documentation on check_ped
  
  josue.chinchilla
  authored and
  josue.chinchilla
  committed
  0a13483
Commits on Apr 27, 2026
- updated error handling and reporting for check_ped
  
  josue.chinchilla
  authored and
  josue.chinchilla
  committed
  9bbc507
- updated parentage functions to work allow user to display NA or not, and to plot results.
  
  josue.chinchilla
  authored and
  josue.chinchilla
  committed
  f798362
- Made edits suggested by autopilot
  
  josue.chinchilla
  authored and
  josue.chinchilla
  committed
  03725d8
- added edits suggested by copilot
  
  josue.chinchilla
  authored and
  josue.chinchilla
  committed
  506a47f
Commits on Apr 28, 2026
- modified default params
  
  josue.chinchilla
  authored and
  josue.chinchilla
  committed
  977e070
- Added authors fror functions and made headers concise
  
  josue.chinchilla
  authored and
  josue.chinchilla
  committed
  5db5fa2
Commits on May 20, 2026
- staged comments for next push
  
  josue.chinchilla
  authored and
  josue.chinchilla
  committed
  6b84e18
- removed zip option and added specific correction arguments
  
  josue.chinchilla
  authored and
  josue.chinchilla
  committed
  4eb79bb
Commits on May 22, 2026
- finalzied refactoring according to CRAN standards
  
  josue.chinchilla
  authored and
  josue.chinchilla
  committed
  1fb19d0
- Updated functions and descriptions to be CRAN compliant and updatede documentations
  
  josue.chinchilla
  authored and
  josue.chinchilla
  committed
  65d48fd
Commits on May 26, 2026
- updated parentage functions to standardize inputs and outputs
  
  josue.chinchilla
  authored and
  josue.chinchilla
  committed
  9b16038
- updated functions to work as a workflow accepting inputs from objects or file paths, updated documentation and test files
  
  josue.chinchilla
  authored and
  josue.chinchilla
  committed
  26bae5f
Commits on May 29, 2026
- updated find_parentage to exlcude self comparison and fix bug of ordering genotype matrices for comparisons. updated test file to accomodate nw arguments
  
  josue.chinchilla
  authored and
  josue.chinchilla
  committed
  7e34dfe
Commits on Jun 1, 2026
- Refactor SNP ID parsing to use regex extraction
  alex-sandercock
  authored
  e2bdef5
- Bump version from 0.7.0 to 0.8.0
  alex-sandercock
  authored
  ef9bd78
Commits on Jun 2, 2026
- updated documentation to include updates to find_parentage
  
  josue.chinchilla
  authored and
  josue.chinchilla
  committed
  bd54c9a
- Merge pull request #63 from Breeding-Insight/update_updog2vcf
  alex-sandercock
  authored
  bdd540b
Commits on Jun 5, 2026
- Merge branch 'development' into add_parentage_functions
  alex-sandercock
  authored
  90af9c4
- Merge pull request #64 from Breeding-Insight/add_parentage_functions
  alex-sandercock
  authored
  7707dcd
Commits on Jun 19, 2026
- Fix madc2vcf_all() crash on off-target alleles with no remaining mismatches
  shbrainard
  committed
  b4ec294
Commits on Jun 24, 2026
- Remove bad POS
  alex-sandercock
  committed
  154d879
- remove BIGpopA functions
  alex-sandercock
  committed
  0453d12
Commits on Jul 2, 2026
Commits on Aug 5, 2026
- init SAT-151
  
  Cristianetaniguti
  authored and
  alex-sandercock
  committed
  8784a7d
- Let pass identical IUPAC code in Ref Alt
  
  Cristianetaniguti
  authored and
  alex-sandercock
  committed
  e0a903f
- SAT-111 SAT-188
  
  Cristianetaniguti
  authored and
  alex-sandercock
  committed
  3d28c45
- adapt tests
  
  Cristianetaniguti
  authored and
  alex-sandercock
  committed
  cf5fa39
- up version
  
  Cristianetaniguti
  authored and
  alex-sandercock
  committed
  be99360
- adopt copilot suggestions
  
  Cristianetaniguti
  authored and
  alex-sandercock
  committed
  c7da438
- adopt more copilot suggestions
  
  Cristianetaniguti
  authored and
  alex-sandercock
  committed
  cdcca73
- bugfix
  
  Cristianetaniguti
  authored and
  alex-sandercock
  committed
  e02e383
- address minors
  
  Cristianetaniguti
  authored and
  alex-sandercock
  committed
  a851de7
- Fixed scientific notation fail
  alex-sandercock
  committed
  6f18e9d
- fixed INFO retrieval
  alex-sandercock
  committed
  e1e7fce
- updated filterVCF documentation
  alex-sandercock
  committed
  9448625
- fixed NA gap
  alex-sandercock
  committed
  cbcfb19
- Merge pull request #68 from Breeding-Insight/filterVCF_updates
  alex-sandercock
  authored
  d4f0029
- Update citation for BIGr in README
  alex-sandercock
  authored
  9e17245

Commits

Commits on Apr 22, 2026

Commits on Apr 24, 2026

Commits on Apr 27, 2026

Commits on Apr 28, 2026

Commits on May 20, 2026

Commits on May 22, 2026

Commits on May 26, 2026

Commits on May 29, 2026

Commits on Jun 1, 2026

Commits on Jun 2, 2026

Commits on Jun 5, 2026

Commits on Jun 19, 2026

Commits on Jun 24, 2026

Commits on Jul 2, 2026

Commits on Aug 5, 2026