Grape#66
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CRAN Updates
Updated funding source and note about BIGr development.
CRAN 7.2 submission
…atches
When add_others = TRUE, compare() computed other_ref_base/other_alt_base with
substring() before checking that any mismatch positions remained. If an off-target
("Other") allele aligns to the reference with its only mismatch at the target SNP
position, that position is removed and pos_ref_idx/pos_alt_idx become integer(0),
so substring() errors with "invalid substring arguments" and the whole run aborts.
Move the two substring() calls inside the existing 'if (length(pos_ref_idx) > 0)'
guard, mirroring how the off-target Match alleles are already handled. Behavior is
unchanged when mismatch positions remain; existing madc2vcf_all tests still pass.
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Pull request overview
This PR streamlines the BIGr R package by removing several legacy/public pedigree-parentage and polyploid breed-composition functions (and their tests/docs), cleaning up dependencies/metadata, and hardening VCF POS handling in madc2vcf_* outputs to avoid scientific notation and invalid/negative coordinates.
Changes:
- Enforces integer, non-negative VCF
POSvalues and drops records with invalidPOSinmadc2vcf_targets()andmadc2vcf_all(). - Removes unused/unmaintained exported functions (
validate_pedigree,find_parentage,check_ped,allele_freq_poly,solve_composition_poly) plus associated tests and man pages. - Updates
DESCRIPTION/NAMESPACEto reflect current dependencies/exports and bumps package version.
Reviewed changes
Copilot reviewed 18 out of 18 changed files in this pull request and generated 2 comments.
Show a summary per file
| File | Description |
|---|---|
| DESCRIPTION | Updates package metadata, dependency lists, and version. |
| NAMESPACE | Removes exports/imports for deleted legacy functions and prunes unused imports. |
| R/madc2vcf_all.R | Normalizes/sanitizes POS (numeric parse, drop invalid, stable sort, format as integer). |
| R/madc2vcf_targets.R | Normalizes/sanitizes POS (numeric parse, drop invalid, stable sort, format as integer) and adds setNames import. |
| R/breedtools_functions.R | Removes legacy breedTools polyploid composition utilities. |
| R/check_ped.R | Removes legacy pedigree QC/correction utility. |
| R/find_parentage.R | Removes legacy parentage assignment utility. |
| R/validate_pedigree.R | Removes legacy trio validation utility. |
| dev/dev_history.R | Adjusts dev workflow script (now executes attachment::att_amend_desc()). |
| man/allele_freq_poly.Rd | Removes documentation for deleted exported function. |
| man/check_ped.Rd | Removes documentation for deleted exported function. |
| man/find_parentage.Rd | Removes documentation for deleted exported function. |
| man/solve_composition_poly.Rd | Removes documentation for deleted exported function. |
| man/validate_pedigree.Rd | Removes documentation for deleted exported function. |
| tests/testthat/test-breedtools_poly.R | Removes tests for deleted breedTools functions. |
| tests/testthat/test-check_ped.R | Removes tests for deleted check_ped(). |
| tests/testthat/test-find_parentage.R | Removes tests for deleted find_parentage(). |
| tests/testthat/test-validate_pedigree.R | Removes tests for deleted validate_pedigree(). |
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| comment = "Breeding Insight")) | ||
| Title: Breeding Insight Genomics Functions for Polyploid and Diploid | ||
| Species | ||
| Version: 0.8.1 |
| # Update dependencies in DESCRIPTION | ||
| # install.packages('attachment', repos = 'https://thinkr-open.r-universe.dev') | ||
| #attachment::att_amend_desc() | ||
| attachment::att_amend_desc() |
Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## development #66 +/- ##
===============================================
- Coverage 81.87% 81.11% -0.77%
===============================================
Files 23 19 -4
Lines 2886 2277 -609
===============================================
- Hits 2363 1847 -516
+ Misses 523 430 -93 ☔ View full report in Codecov by Harness. 🚀 New features to boost your workflow:
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…tring Fix madc2vcf_all() "invalid substring arguments" error on off-target alleles
Cristianetaniguti
approved these changes
Jul 2, 2026
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This pull request makes significant changes to the BIGr package, primarily focused on cleaning up the codebase and dependencies by removing several unused or unnecessary functions and packages. It also updates the package metadata and dependencies for improved clarity and maintainability.
Key changes include:
Updated madc2vcf_all and madc2vcf_targets
Removal of unused functions and dependencies
allele_freq_poly,solve_composition_poly, andcheck_pedfrom the codebase and from the list of exported functions in theNAMESPACEfile, as well as their associated documentation. These functions are no longer maintained or required in the package. [1] [2] [3] [4]data.table,janitor, andquadprogpackages from theNAMESPACEfile, as they are no longer needed after the function removals. [1] [2]Updates to package metadata and dependencies
DESCRIPTIONfile to increment the version to 0.8.1, clarify the package title and description, and clean up the list of imports and suggests to accurately reflect current dependencies. Also updated formatting and moved some entries for consistency.These changes streamline the BIGr package by removing legacy or redundant code and ensuring that only necessary dependencies are included, which should improve maintainability and reduce potential conflicts.