Add parentage functions by josuechinchilla · Pull Request #55 · Breeding-Insight/BIGr

josuechinchilla · 2026-04-06T17:40:33Z

Added 2 parentage functions along with the test files and updated package giles to include updates

…t/BIGr into ped_indels_update

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

Madc2vcf updates

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

…ht/BIGr into ped_indels_update

josuechinchilla · 2026-04-06T17:44:20Z

requested pull to main by mistake. Closed.

Copilot

Pull request overview

Adds new parentage and MADC→VCF utilities, expands MADC sanity-checking, and significantly extends the package test suite/documentation for these workflows.

Changes:

Introduces new parentage functions (validate_pedigree(), find_parentage()) plus tests.
Adds madc2vcf_multi() (polyRAD pipeline) and expands MADC preprocessing/sanity checks and count extraction options.
Updates existing utilities/docs/tests (e.g., filterVCF(), imputation_concordance(), CI deps, NEWS/DESCRIPTION/NAMESPACE).

Reviewed changes

Copilot reviewed 38 out of 39 changed files in this pull request and generated 18 comments.

Show a summary per file

File	Description
R/validate_pedigree.R	New trio validation + correction outputs
R/find_parentage.R	New parentage assignment (single-parent + best-pair)
R/madc2vcf_multi.R	New MADC→VCF conversion via polyRAD
R/check_madc_sanity.R	New MADC sanity-check function + `check_botloci()`
R/get_countsMADC.R	Extends count extraction to accept in-memory MADC + collapse matches
R/imputation_concordance.R	Adds plotting/printing options + doc expansion
R/filterVCF.R	Adds optional pre-filter quality metrics output
R/check_ped.R	Refactors pedigree checking and reporting behavior
R/utils.R	Adds `vmsg()` + `url_exists()` helper
tests/testthat/test-validate_pedigree.R	New validate_pedigree tests
tests/testthat/test-find_parentage.R	New find_parentage tests
tests/testthat/test-madc2vcf_targets.R	Expands tests for REF/ALT recovery + external fixture coverage
tests/testthat/test-madc2vcf_all.R	Expands tests for `madc2vcf_all` (external fixtures)
tests/testthat/test-madc2vcf_multi.R	Adds tests for `madc2vcf_multi` (external fixtures)
tests/testthat/test-check_madc_sanity.R	Adds tests for `check_madc_sanity()`
tests/testthat/test-check_ped.R	Updates expectations for revised `check_ped()` output
tests/testthat/test-imputation_concordance.R	Minor whitespace cleanup
man/validate_pedigree.Rd	New docs for validate_pedigree
man/find_parentage.Rd	New docs for find_parentage
man/madc2vcf_multi.Rd	New docs for madc2vcf_multi
man/check_madc_sanity.Rd	New docs for check_madc_sanity
man/vmsg.Rd	New docs for vmsg
man/get_countsMADC.Rd	Updates docs for new get_countsMADC signature
man/get_counts.Rd	New internal docs for get_counts
man/madc2vcf_targets.Rd	Updates docs for new args/behavior
man/madc2vcf_all.Rd	Updates docs for required args + others/markers_info
man/imputation_concordance.Rd	Updates docs for new args/return semantics
man/filterVCF.Rd	Documents new `quality.rates` argument
man/check_ped.Rd	Updates docs for revised check_ped behavior
NEWS.md	Adds release notes for 0.7.0 and interim versions
DESCRIPTION	Bumps version; updates imports/suggests + metadata
NAMESPACE	Exports new functions + imports ggplot2/data.table symbols
.github/workflows/R-CMD-check.yaml	Installs new suggested deps in CI
.gitignore	Ignores `.DS_Store`
BIGr.Rproj	Adds ProjectId

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Copilot · 2026-04-06T17:46:04Z

+  genos_mat <- as.matrix(genos, rownames = "ID")
+
+  # Create homozygous-only matrix for parent analysis
+  genos_hom <- copy(genos)
+  marker_cols <- setdiff(names(genos_hom), "ID")
+  for (col in marker_cols) {
+    genos_hom[get(col) == 1, (col) := NA_integer_]
+  }
+  genos_hom_mat <- as.matrix(genos_hom, rownames = "ID")


as.matrix(genos, rownames = "ID") (and the similar call for genos_hom) is not a valid base R as.matrix() usage for a data.frame/data.table and will error because the rownames argument is not supported. Build the matrix from marker columns and then set rownames(mat) <- genos$ID (and likewise for genos_hom).

Suggested change

genos_mat <- as.matrix(genos, rownames = "ID")

# Create homozygous-only matrix for parent analysis

genos_hom <- copy(genos)

marker_cols <- setdiff(names(genos_hom), "ID")

for (col in marker_cols) {

genos_hom[get(col) == 1, (col) := NA_integer_]

}

genos_hom_mat <- as.matrix(genos_hom, rownames = "ID")

marker_cols <- setdiff(names(genos), "ID")

genos_mat <- as.matrix(genos[, ..marker_cols])

rownames(genos_mat) <- genos$ID

# Create homozygous-only matrix for parent analysis

genos_hom <- copy(genos)

for (col in marker_cols) {

genos_hom[get(col) == 1, (col) := NA_integer_]

}

genos_hom_mat <- as.matrix(genos_hom[, ..marker_cols])

rownames(genos_hom_mat) <- genos_hom$ID

Copilot · 2026-04-06T17:46:04Z

+      comparisons <- sum(!is.na(cand_hom) & !is.na(prog_hom))
+      if (comparisons == 0) return(NA_real_)
+      (sum(cand_hom != prog_hom, na.rm = TRUE) / comparisons) * 100
+    })


find_best_parent() uses which.min(errors) without handling the case where all candidate error rates are NA (e.g., no comparable homozygous markers for any candidate). In that case which.min() returns integer(0) and indexing candidates[best_idx] yields character(0), which can break downstream assignments. Add an explicit if (all(is.na(errors))) early return with NA id/error_pct.

Suggested change

})

})

if (all(is.na(errors))) return(list(id = NA_character_, error_pct = NA_real_))

Copilot · 2026-04-06T17:46:05Z

+test_that("error_threshold out of range raises an error", {
+  f <- write_temp_files()
+  expect_error(validate_pedigree(f$ped, f$genos, error_threshold = 150,
+                                 verbose = FALSE, write_txt = FALSE))
+  expect_error(validate_pedigree(f$ped, f$genos, error_threshold = -1,
+                                 verbose = FALSE, write_txt = FALSE))
+})
+
+test_that("homozygous_threshold out of range raises an error", {
+  f <- write_temp_files()
+  expect_error(validate_pedigree(f$ped, f$genos, homozygous_threshold = 101,
+                                 verbose = FALSE, write_txt = FALSE))
+  expect_error(validate_pedigree(f$ped, f$genos, homozygous_threshold = -5,
+                                 verbose = FALSE, write_txt = FALSE))


The tests call validate_pedigree(..., error_threshold=...) and homozygous_threshold=..., but the function signature uses trio_error_threshold and single_parent_error_threshold. This will currently fail with “unused argument” errors. Update the tests to use the correct argument names, or add backwards-compatible aliases in validate_pedigree().

Copilot · 2026-04-06T17:46:05Z

+
+  #### Logic for Best Pair Method ####
+  if (method == "best.pair") {
+    genos_mat <- as.matrix(genos, rownames = "ID")


as.matrix(..., rownames = "ID") is not supported for data.frame/data.table and will error. Convert only the marker columns to a matrix and then set rownames() from the ID column (same for genos_hom and for the genos_mat used in the best.pair branch).

Suggested change

genos_mat <- as.matrix(genos, rownames = "ID")

genos_mat <- as.matrix(genos[, !names(genos) %in% "ID", with = FALSE])

rownames(genos_mat) <- genos$ID

Copilot · 2026-04-06T17:46:05Z

+  sire_candidates <- all_parents[Sex %in% c("M", "A", "NA"), .SD]
+  dam_candidates <- all_parents[Sex %in% c("F", "A", "NA")]


Sex %in% c("M", "A", "NA") will not keep rows where Sex is actually NA (missing), because NA %in% ... evaluates to NA and filters out. If the intent is to treat missing sex as ambiguous, include an is.na(Sex) branch (or set missing Sex to "A" after toupper).

Suggested change

sire_candidates <- all_parents[Sex %in% c("M", "A", "NA"), .SD]

dam_candidates <- all_parents[Sex %in% c("F", "A", "NA")]

sire_candidates <- all_parents[is.na(Sex) | Sex %in% c("M", "A", "NA"), .SD]

dam_candidates <- all_parents[is.na(Sex) | Sex %in% c("F", "A", "NA")]

Copilot · 2026-04-06T17:46:07Z

+test_that("simu alfalfa",{
+
+  github_path <- "https://raw.githubusercontent.com/Breeding-Insight/BIGapp-PanelHub/refs/heads/long_seq/"
+
+  # External alfalfa test files
+  alfalfa_madc           <- paste0(github_path, "test_madcs/alfalfa_madc.csv")
+  alfalfa_madc_wrongID   <- paste0(github_path, "test_madcs/alfalfa_madc_wrongID.csv")
+  alfalfa_madc_raw       <- paste0(github_path, "test_madcs/alfalfa_madc_raw.csv")       # raw DArT format (7-row header)
+  alfalfa_iupac          <- paste0(github_path, "test_madcs/alfalfa_IUPAC.csv")
+  alfalfa_lowercase      <- paste0(github_path, "test_madcs/alfalfa_lowercase.csv")
+  alfalfa_botloci        <- paste0(github_path, "alfalfa/20201030-BI-Alfalfa_SNPs_DArTag-probe-design_f180bp.botloci")          # botloci for alfalfa
+  alfalfa_markers_info   <- paste0(github_path, "alfalfa/20201030-BI-Alfalfa_SNPs_DArTag-probe-design_snpID_lut.csv") # markers_info: CloneID/BI_markerID, Chr, Pos, Ref, Alt
+  alfalfa_markers_info_ChromPos   <- paste0(github_path, "test_madcs/alfalfa_marker_info_ChromPos.csv") # markers_info: CloneID/BI_markerID, Chr, Pos
+
+
+  # External potato test files
+  potato_indel_madc                 <- paste0(github_path, "test_madcs/potato_indel_madc.csv")
+  potato_indel_iupac                <- paste0(github_path, "test_madcs/potato_indel_IUPAC.csv")
+  potato_indel_lowercase            <- paste0(github_path, "test_madcs/potato_indel_lowercase.csv")
+  potato_more_indels_chrompos_false <- paste0(github_path, "test_madcs/potato_more_indels_madc_ChromPosFALSE.csv")
+  potato_botloci                    <- paste0(github_path, "potato/potato_dartag_v2_3915markers_rm7dupTags_6traitMarkers_f150bp_ref_alt.botloci")
+  potato_markers_info               <- paste0(github_path, "potato/potato_dartag_v2_3915markers_rm7dupTags_6traitMarkers_rm1dup_snpID_lut.csv") # CloneID/BI_markerID, Chr, Pos, Ref, Alt
+  potato_markers_info_ChromPos   <- paste0(github_path, "test_madcs/potato_marker_info_chrompos.csv") # markers_info: CloneID/BI_markerID, Chr, Pos
+
+  skip_if_offline("raw.githubusercontent.com")
+


These tests depend on downloading external files from raw.githubusercontent.com (a moving branch URL). Even with skip_if_offline(), this makes CI/CRAN runs flaky and can violate the “no network in tests” expectation. Prefer vendoring minimal fixtures into tests/testthat/ (or using with_mocked_bindings()), and keep any integration test behind an explicit opt-in env var.

Copilot · 2026-04-06T17:46:07Z

+test_that("simu alfalfa",{
+
+  github_path <- "https://raw.githubusercontent.com/Breeding-Insight/BIGapp-PanelHub/refs/heads/long_seq/"
+
+  # External alfalfa test files
+  alfalfa_madc           <- paste0(github_path, "test_madcs/alfalfa_madc.csv")
+  alfalfa_madc_wrongID   <- paste0(github_path, "test_madcs/alfalfa_madc_wrongID.csv")
+  alfalfa_madc_raw       <- paste0(github_path, "test_madcs/alfalfa_madc_raw.csv")       # raw DArT format (7-row header)
+  alfalfa_iupac          <- paste0(github_path, "test_madcs/alfalfa_IUPAC.csv")
+  alfalfa_lowercase      <- paste0(github_path, "test_madcs/alfalfa_lowercase.csv")
+  alfalfa_botloci        <- paste0(github_path, "alfalfa/20201030-BI-Alfalfa_SNPs_DArTag-probe-design_f180bp.botloci")          # botloci for alfalfa
+  alfalfa_markers_info   <- paste0(github_path, "alfalfa/20201030-BI-Alfalfa_SNPs_DArTag-probe-design_snpID_lut.csv") # markers_info: CloneID/BI_markerID, Chr, Pos, Ref, Alt
+  alfalfa_markers_info_ChromPos   <- paste0(github_path, "test_madcs/alfalfa_marker_info_ChromPos.csv") # markers_info: CloneID/BI_markerID, Chr, Pos
+
+
+  # External potato test files
+  potato_indel_madc                 <- paste0(github_path, "test_madcs/potato_indel_madc.csv")
+  potato_indel_iupac                <- paste0(github_path, "test_madcs/potato_indel_IUPAC.csv")
+  potato_indel_lowercase            <- paste0(github_path, "test_madcs/potato_indel_lowercase.csv")
+  potato_more_indels_chrompos_false <- paste0(github_path, "test_madcs/potato_more_indels_madc_ChromPosFALSE.csv")
+  potato_botloci                    <- paste0(github_path, "potato/potato_dartag_v2_3915markers_rm7dupTags_6traitMarkers_f150bp_ref_alt.botloci")
+  potato_markers_info               <- paste0(github_path, "potato/potato_dartag_v2_3915markers_rm7dupTags_6traitMarkers_rm1dup_snpID_lut.csv") # CloneID/BI_markerID, Chr, Pos, Ref, Alt
+  potato_markers_info_ChromPos   <- paste0(github_path, "test_madcs/potato_marker_info_chrompos.csv") # markers_info: CloneID/BI_markerID, Chr, Pos
+
+  skip_if_offline("raw.githubusercontent.com")
+
+  test_that("ALFALFA — clean fixed allele ID MADC", {
+    out <- tempfile(fileext = ".vcf")
+    expect_no_error(


There are multiple test_that() calls nested inside another test_that() block. Nested test_that() is not supported reliably by testthat and can cause tests to be skipped or error in unexpected ways. Flatten these into top-level test_that() blocks (or use helper functions within a single test).

Copilot · 2026-04-06T17:46:08Z

+test_that("simu alfalfa",{
+
+  github_path <- "https://raw.githubusercontent.com/Breeding-Insight/BIGapp-PanelHub/refs/heads/long_seq/"
+
+  # External alfalfa test files
+  alfalfa_madc           <- paste0(github_path, "test_madcs/alfalfa_madc.csv")
+  alfalfa_madc_wrongID   <- paste0(github_path, "test_madcs/alfalfa_madc_wrongID.csv")
+  alfalfa_madc_raw       <- paste0(github_path, "test_madcs/alfalfa_madc_raw.csv")       # raw DArT format (7-row header)
+  alfalfa_iupac          <- paste0(github_path, "test_madcs/alfalfa_IUPAC.csv")
+  alfalfa_lowercase      <- paste0(github_path, "test_madcs/alfalfa_lowercase.csv")
+  alfalfa_botloci        <- paste0(github_path, "alfalfa/20201030-BI-Alfalfa_SNPs_DArTag-probe-design_f180bp.botloci")          # botloci for alfalfa
+  alfalfa_markers_info   <- paste0(github_path, "alfalfa/20201030-BI-Alfalfa_SNPs_DArTag-probe-design_snpID_lut.csv") # markers_info: CloneID/BI_markerID, Chr, Pos, Ref, Alt
+  alfalfa_markers_info_ChromPos   <- paste0(github_path, "test_madcs/alfalfa_marker_info_ChromPos.csv") # markers_info: CloneID/BI_markerID, Chr, Pos
+  alfalfa_microhapDB <- paste0(github_path, "alfalfa/alfalfa_allele_db_v001.fa")
+
+  # External potato test files
+  potato_indel_madc                 <- paste0(github_path, "test_madcs/potato_indel_madc.csv")
+  potato_indel_iupac                <- paste0(github_path, "test_madcs/potato_indel_IUPAC.csv")
+  potato_indel_lowercase            <- paste0(github_path, "test_madcs/potato_indel_lowercase.csv")
+  potato_more_indels_chrompos_false <- paste0(github_path, "test_madcs/potato_more_indels_madc_ChromPosFALSE.csv")
+  potato_botloci                    <- paste0(github_path, "potato/potato_dartag_v2_3915markers_rm7dupTags_6traitMarkers_f150bp_ref_alt.botloci")
+  potato_markers_info               <- paste0(github_path, "potato/potato_dartag_v2_3915markers_rm7dupTags_6traitMarkers_rm1dup_snpID_lut.csv") # CloneID/BI_markerID, Chr, Pos, Ref, Alt
+  potato_markers_info_ChromPos   <- paste0(github_path, "test_madcs/potato_marker_info_chrompos.csv") # markers_info: CloneID/BI_markerID, Chr, Pos
+  potato_microhapDB <- paste0(github_path, "potato/potato_allele_db_v001.fa")
+
+  skip_if_offline("raw.githubusercontent.com")
+


This test block also downloads external fixtures from GitHub at runtime. That makes test runs flaky and can break when the referenced branch/files change. Consider shipping stable fixtures with the package and removing network dependence from unit tests.

Copilot · 2026-04-06T17:46:08Z

+test_that("simu alfalfa",{
+
+  github_path <- "https://raw.githubusercontent.com/Breeding-Insight/BIGapp-PanelHub/refs/heads/long_seq/"
+
+  # External alfalfa test files
+  alfalfa_madc           <- paste0(github_path, "test_madcs/alfalfa_madc.csv")
+  alfalfa_madc_wrongID   <- paste0(github_path, "test_madcs/alfalfa_madc_wrongID.csv")
+  alfalfa_madc_raw       <- paste0(github_path, "test_madcs/alfalfa_madc_raw.csv")       # raw DArT format (7-row header)
+  alfalfa_iupac          <- paste0(github_path, "test_madcs/alfalfa_IUPAC.csv")
+  alfalfa_lowercase      <- paste0(github_path, "test_madcs/alfalfa_lowercase.csv")
+  alfalfa_botloci        <- paste0(github_path, "alfalfa/20201030-BI-Alfalfa_SNPs_DArTag-probe-design_f180bp.botloci")          # botloci for alfalfa
+  alfalfa_markers_info   <- paste0(github_path, "alfalfa/20201030-BI-Alfalfa_SNPs_DArTag-probe-design_snpID_lut.csv") # markers_info: CloneID/BI_markerID, Chr, Pos, Ref, Alt
+  alfalfa_markers_info_ChromPos   <- paste0(github_path, "test_madcs/alfalfa_marker_info_ChromPos.csv") # markers_info: CloneID/BI_markerID, Chr, Pos
+  alfalfa_microhapDB <- paste0(github_path, "alfalfa/alfalfa_allele_db_v001.fa")
+
+  # External potato test files
+  potato_indel_madc                 <- paste0(github_path, "test_madcs/potato_indel_madc.csv")
+  potato_indel_iupac                <- paste0(github_path, "test_madcs/potato_indel_IUPAC.csv")
+  potato_indel_lowercase            <- paste0(github_path, "test_madcs/potato_indel_lowercase.csv")
+  potato_more_indels_chrompos_false <- paste0(github_path, "test_madcs/potato_more_indels_madc_ChromPosFALSE.csv")
+  potato_botloci                    <- paste0(github_path, "potato/potato_dartag_v2_3915markers_rm7dupTags_6traitMarkers_f150bp_ref_alt.botloci")
+  potato_markers_info               <- paste0(github_path, "potato/potato_dartag_v2_3915markers_rm7dupTags_6traitMarkers_rm1dup_snpID_lut.csv") # CloneID/BI_markerID, Chr, Pos, Ref, Alt
+  potato_markers_info_ChromPos   <- paste0(github_path, "test_madcs/potato_marker_info_chrompos.csv") # markers_info: CloneID/BI_markerID, Chr, Pos
+  potato_microhapDB <- paste0(github_path, "potato/potato_allele_db_v001.fa")
+
+  skip_if_offline("raw.githubusercontent.com")
+
+  test_that("ALFALFA — clean fixed allele ID MADC", {
+    out <- tempfile(fileext = ".vcf")
+    #out <- "test.vcf"
+    # Default parameters
+    expect_no_error(
+      madc2vcf_all(madc = alfalfa_madc,


Like test-madc2vcf_targets.R, this file nests multiple test_that() calls inside another test_that() block (the outer "simu alfalfa" test). This pattern is not reliably supported by testthat; split into separate top-level tests.

Copilot · 2026-04-06T17:46:08Z

+ github_path <- "https://raw.githubusercontent.com/Breeding-Insight/BIGapp-PanelHub/refs/heads/long_seq/"
+
+  # External alfalfa test files
+  alfalfa_madc           <- paste0(github_path, "test_madcs/alfalfa_madc.csv")
+  alfalfa_madc_wrongID   <- paste0(github_path, "test_madcs/alfalfa_madc_wrongID.csv")
+  alfalfa_madc_raw       <- paste0(github_path, "test_madcs/alfalfa_madc_raw.csv")       # raw DArT format (7-row header)
+  alfalfa_iupac          <- paste0(github_path, "test_madcs/alfalfa_IUPAC.csv")
+  alfalfa_lowercase      <- paste0(github_path, "test_madcs/alfalfa_lowercase.csv")
+  alfalfa_botloci        <- paste0(github_path, "alfalfa/20201030-BI-Alfalfa_SNPs_DArTag-probe-design_f180bp.botloci")          # botloci for alfalfa
+  alfalfa_markers_info   <- paste0(github_path, "alfalfa/20201030-BI-Alfalfa_SNPs_DArTag-probe-design_snpID_lut.csv") # markers_info: CloneID/BI_markerID, Chr, Pos, Ref, Alt
+  alfalfa_markers_info_ChromPos   <- paste0(github_path, "test_madcs/alfalfa_marker_info_ChromPos.csv") # markers_info: CloneID/BI_markerID, Chr, Pos
+  alfalfa_microhapDB <- paste0(github_path, "alfalfa/alfalfa_allele_db_v001.fa")
+
+  # External potato test files
+  potato_indel_madc                 <- paste0(github_path, "test_madcs/potato_indel_madc.csv")
+  potato_indel_iupac                <- paste0(github_path, "test_madcs/potato_indel_IUPAC.csv")
+  potato_indel_lowercase            <- paste0(github_path, "test_madcs/potato_indel_lowercase.csv")
+  potato_more_indels_chrompos_false <- paste0(github_path, "test_madcs/potato_more_indels_madc_ChromPosFALSE.csv")
+  potato_botloci                    <- paste0(github_path, "potato/potato_dartag_v2_3915markers_rm7dupTags_6traitMarkers_f150bp_ref_alt.botloci")
+  potato_markers_info               <- paste0(github_path, "potato/potato_dartag_v2_3915markers_rm7dupTags_6traitMarkers_rm1dup_snpID_lut.csv") # CloneID/BI_markerID, Chr, Pos, Ref, Alt
+  potato_markers_info_ChromPos   <- paste0(github_path, "test_madcs/potato_marker_info_chrompos.csv") # markers_info: CloneID/BI_markerID, Chr, Pos
+  potato_microhapDB <- paste0(github_path, "potato/potato_allele_db_v001.fa")
+
+  skip_if_offline("raw.githubusercontent.com")
+


This test uses external GitHub-hosted fixtures at runtime. Even with skip_if_offline(), it introduces non-determinism and can fail if the remote branch changes or is rate-limited. Prefer local fixtures for unit tests; keep any online integration test behind an explicit opt-in flag.

Cristianetaniguti and others added 30 commits October 3, 2025 15:11

indels support for madc2vcf_targets

778aefa

updated check_ped to save corrected dataframe and report

1b761b9

reorganized report and fixed language

743043a

bugfix - if hapDB padding is not matching report

0b97b46

add indel exception

bccf0ac

bugfix

25caf0a

up version

4f30e52

added option to print plot or list to imputation_concordance

82279af

ignore DS_STore

6b81982

added option to print pre-filtering depth and genotyping rate

8205e4e

added calculation for Ho

31248e3

up version

757b01c

Merge branch 'check_ped_update' of https://github.com/Breeding-Insigh…

0934210

…t/BIGr into ped_indels_update

merge dev branches

e18b2c6

Merge branch 'development' into ped_indels_update

768ab93

opt messages

5c0b590

messages ok

9afb265

targets okay

c31118d

targets ok

5d54f0d

Potential fix for pull request finding

ee50981

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Potential fix for pull request finding

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Potential fix for pull request finding

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Merge branch 'ped_indels_update' into madc2vcf_all_updates

7c12d49

Merge pull request #53 from Breeding-Insight/madc2vcf_all_updates

df6fe92

Madc2vcf updates

Update R/madc2vcf_targets.R

6059c10

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

Update R/check_madc_sanity.R

b09b0c1

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

Update R/get_countsMADC.R

409dbd3

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Update R/get_countsMADC.R

e6fce19

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Update R/check_madc_sanity.R

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Cristianetaniguti and others added 22 commits March 27, 2026 10:50

fix tests

bbfbee2

Merge branch 'ped_indels_update' of https://github.com/Breeding-Insig…

38c3564

…ht/BIGr into ped_indels_update

madc2vcf_all indels support okay

55ee61a

madc2vcf_all support indel

bf5ff4c

add support for Others

291ae8e

up version

84852da

add madc2vcf_multi

96a4ed1

fix checks

cec168d

fix checks 2

0be2e0f

add VariantAnnotation to test env

33fc87c

ignore madc2vcf_multi tests in actions

77107ba

more messages and tests

ccf9e77

bugfix

8a00c9e

update man

f2013e3

minor version up

b01c12b

added v1 of parentage function

d0e02e2

modified code to use data.table for increased efficiency

5baae79

improved assign_parentage and validate_parentage

a252f22

finalized parentage functions for diploids and test files

bf0a468

Added parentage functions and updated associated files

01e943d

updated headers and importFrom for functions along iwth namespace

8ee65a3

deleted cra check files

e5b2004

josuechinchilla requested review from alex-sandercock and Copilot April 6, 2026 17:40

josuechinchilla closed this Apr 6, 2026

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Add parentage functions#55

Add parentage functions#55
josuechinchilla wants to merge 52 commits intomainfrom
add_parentage_functions

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	})
	})
	if (all(is.na(errors))) return(list(id = NA_character_, error_pct = NA_real_))

	genos_mat <- as.matrix(genos, rownames = "ID")
	genos_mat <- as.matrix(genos[, !names(genos) %in% "ID", with = FALSE])
	rownames(genos_mat) <- genos$ID

		sire_candidates <- all_parents[Sex %in% c("M", "A", "NA"), .SD]
		dam_candidates <- all_parents[Sex %in% c("F", "A", "NA")]

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