Development by josuechinchilla · Pull Request #58 · Breeding-Insight/BIGr

josuechinchilla · 2026-04-22T17:21:59Z

Added original parentage functions and updated those to fit Meng's feedback

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Madc2vcf and Pedigree functions updates

Copilot

Pull request overview

This PR improves the MADC→VCF conversion utilities and related sanity checks, adds regression tests for edge cases (sample name preservation, markers_info ID matching, AD formatting), and updates package metadata/docs for optional dependencies and internal helpers.

Changes:

Add tests covering sample-name preservation, missing-column error surfacing, AD formatting, and markers_info ID remapping behavior.
Make sanity-check reporting robust to NA checks and add Marker_ID support via a shared ID-column picker helper.
Update docs and package metadata: make ggplot2/polyRAD optional at runtime, and adjust exported/internal utilities.

Reviewed changes

Copilot reviewed 21 out of 21 changed files in this pull request and generated 7 comments.

Show a summary per file

File	Description
tests/testthat/test-madc2vcf_targets.R	Adds regression tests for sample names and missing-column errors; updates expected error text.
tests/testthat/test-madc2vcf_all.R	Adds regression tests for AD formatting, BI_markerID matching behavior, and missing-column errors; loosens one error regex.
tests/testthat/test-check_madc_sanity.R	Adds skip-if-offline and several new tests around botloci remapping/padding and ID-column selection.
man/vmsg.Rd	Removes generated documentation for `vmsg()` (now treated as internal).
man/madc2vcf_targets.Rd	Updates parameter docs to reflect Marker_ID support and botloci/markers_info requirements.
man/madc2vcf_multi.Rd	Updates description to reflect multiallelic/microhaplotype pipeline wording.
man/imputation_concordance.Rd	Replaces `\dontrun{}` example with runnable example data and call.
man/get_countsMADC.Rd	Updates `\seealso{}` to remove link to internal `get_counts()`.
man/get_counts.Rd	Removes generated documentation for internal `get_counts()`.
man/filterVCF.Rd	Removes `quality.rates` argument docs and updates examples.
man/check_madc_sanity.Rd	Documents the new `OtherAlleles` check.
R/utils.R	Converts `vmsg()` roxygen to `@noRd` (internal) and minor formatting cleanup.
R/madc2vcf_targets.R	Preserves original column names (`check.names=FALSE`), handles `NA` checks safely, and uses shared ID-column picking (CloneID/Marker_ID/BI_markerID).
R/madc2vcf_multi.R	Makes sanity-check messaging robust to `NA` and adds a runtime check for optional `polyRAD`.
R/madc2vcf_all.R	Makes sanity-check messaging robust to `NA`, improves markers_info ID matching logic, and fixes AD formatting for biallelic targets.
R/imputation_concordance.R	Removes ggplot2 import reliance; uses `ggplot2::` and checks `requireNamespace()` when `plot=TRUE`.
R/get_countsMADC.R	Enforces mutual exclusivity of `madc_file` vs `madc_object`; marks internal `get_counts()` as `@noRd`.
R/filterVCF.R	Removes `quality.rates` functionality and shifts messaging from `cat()` to `message()/warning()`.
R/check_madc_sanity.R	Improves ChromPos validation, adds `pick_markers_info_id_col()`, and enhances `check_botloci()` remapping/padding behavior.
NAMESPACE	Stops exporting `vmsg()` and removes `ggplot2` import.
DESCRIPTION	Moves `ggplot2` to Suggests (optional dependency).

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Copilot · 2026-04-22T17:31:51Z

+ Pos = c(1, 2)
+ )
+
+ res <- check_botloci(botloci, report, ChromPos = FALSE, mi_df = mi_df, verbose = FALSE)


These tests call check_botloci() directly, but check_botloci is not exported in NAMESPACE. testthat::test_check() loads the installed package via library(BIGr), so this will fail with “could not find function” in CI/CRAN. Call it via BIGr:::check_botloci() (or export it if it’s intended to be public).

Copilot · 2026-04-22T17:31:51Z

+ Pos = 123
+ )
+
+ res <- check_botloci(botloci, report, ChromPos = TRUE, mi_df = mi_df, verbose = FALSE)


These tests call check_botloci() directly, but check_botloci is not exported in NAMESPACE. testthat::test_check() loads the installed package via library(BIGr), so this will fail with “could not find function” in CI/CRAN. Call it via BIGr:::check_botloci() (or export it if it’s intended to be public).

Copilot · 2026-04-22T17:31:52Z

+ )
+ query_ids <- c("m1", "m1", "m1", "m2")
+
+ expect_equal(pick_markers_info_id_col(mi_df, query_ids), "CloneID")


This test calls pick_markers_info_id_col() directly, but it is an internal helper (@noRd) and not exported. Under testthat::test_check() (installed package), this will error. Use BIGr:::pick_markers_info_id_col() (or export it if it’s intended to be public/tested).
Suggested change
expect_equal(pick_markers_info_id_col(mi_df, query_ids), "CloneID")
expect_equal(BIGr:::pick_markers_info_id_col(mi_df, query_ids), "CloneID")

Copilot · 2026-04-22T17:31:52Z

+ )
+
+ expect_error(
+ check_botloci(botloci, report, ChromPos = TRUE, verbose = FALSE),


These tests call check_botloci() directly, but check_botloci is not exported in NAMESPACE. testthat::test_check() loads the installed package via library(BIGr), so this will fail with “could not find function” in CI/CRAN. Call it via BIGr:::check_botloci() (or export it if it’s intended to be public).

Copilot · 2026-04-22T17:31:52Z

+ Pos = 1
+ )
+
+ res <- check_botloci(botloci, report, ChromPos = TRUE, mi_df = mi_df, verbose = FALSE)


These tests call check_botloci() directly, but check_botloci is not exported in NAMESPACE. testthat::test_check() loads the installed package via library(BIGr), so this will fail with “could not find function” in CI/CRAN. Call it via BIGr:::check_botloci() (or export it if it’s intended to be public).

Copilot · 2026-04-22T17:31:52Z

 filterVCF <- function(vcf.file,
- quality.rates = FALSE,
- filter.OD = NULL,
- filter.BIAS.min = NULL,
- filter.BIAS.max = NULL,
- filter.DP = NULL,
- filter.MPP = NULL,
- filter.PMC = NULL,
- filter.MAF = NULL,
- filter.SAMPLE.miss = NULL,
- filter.SNP.miss = NULL,
- ploidy,
- output.file = NULL) {
+ filter.OD = NULL,
+ filter.BIAS.min = NULL,
+ filter.BIAS.max = NULL,
+ filter.DP = NULL,
+ filter.MPP = NULL,
+ filter.PMC = NULL,
+ filter.MAF = NULL,
+ filter.SAMPLE.miss = NULL,
+ filter.SNP.miss = NULL,
+ ploidy,
+ output.file = NULL) {


filterVCF() is exported and this change removes the quality.rates argument entirely. That’s a breaking API change for any callers passing quality.rates=.... Consider keeping the parameter (deprecated/no-op with a warning) or accepting ... and warning on quality.rates to preserve backward compatibility for at least one release.

Copilot · 2026-04-22T17:31:53Z

 export(madc2vcf_multi)
 export(madc2vcf_targets)
 export(merge_MADCs)
 export(solve_composition_poly)
 export(thinSNP)


NAMESPACE no longer exports vmsg. If vmsg() was previously part of the public API, this is a breaking change for downstream users. If the intent is to make it internal, consider a deprecation period (keep exporting but mark deprecated) and document the change in NEWS / bump version accordingly.

alex-sandercockand others added 20 commits April 8, 2026 08:40

Fix formatting of RefAltSeqs documentation
4ec471b

updated docs
cb76880

revert filterVCF
ab944e8

support LUT Marker_ID
4ac0c55

Apply suggestion from @Copilot
5234572
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Apply suggestion from @Copilot
8c9dcda
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

covered error case
b4d5534

add example and suggest ggplot
57bbc89

make get_counts internal
4bb67fd

update test
ff1ef84

added marker_id support
86b4fef

fixed AD generation bug
c10d134

improved truth check
1ae386f

support Marker_ID
49cb0a4

Update documentation for verbose message utility
22fc6e4

fix exports
38dd609

skipping if offline
56336da

madc2vcf_multi better function description
089e8fd

roxygenise
8ee0b81

Merge pull request#54from Breeding-Insight/ped_indels_update
c2cba9d
Madc2vcf and Pedigree functions updates

josuechinchilla requested a review from Copilot April 22, 2026 17:22

Copilotstarted reviewing on behalf of josuechinchilla April 22, 2026 17:23 View session

Merge branch 'add_parentage_functions' into development
ccc0952

josuechinchilla merged commit f590dad into add_parentage_functionsApr 22, 2026
4 checks passed

CopilotAI reviewed Apr 22, 2026
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	expect_equal(pick_markers_info_id_col(mi_df, query_ids), "CloneID")
	expect_equal(BIGr:::pick_markers_info_id_col(mi_df, query_ids), "CloneID")

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