Add parentage functions by josuechinchilla · Pull Request #56 · Breeding-Insight/BIGr

josuechinchilla · 2026-04-06T17:45:33Z

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

Copilot

Pull request overview

This PR expands BIGr with new pedigree/parentage utilities and broader updates to MADC→VCF tooling, pedigree QC, and related documentation/tests, culminating in a version bump to 0.7.0.

Changes:

Added new parentage/pedigree functions: find_parentage() and validate_pedigree() with corresponding test coverage.
Added/updated MADC processing utilities (check_madc_sanity, madc2vcf_multi, get_countsMADC/get_counts) plus extensive integration-style tests.
Updated check_ped(), filterVCF(), package metadata, NAMESPACE, NEWS, docs, and CI workflow dependencies.

Reviewed changes

Copilot reviewed 38 out of 39 changed files in this pull request and generated 15 comments.

Show a summary per file

File	Description
R/validate_pedigree.R	New trio validation + correction file writing.
tests/testthat/test-validate_pedigree.R	New unit tests for `validate_pedigree()`.
R/find_parentage.R	New parentage assignment (single-parent + best-pair) logic.
tests/testthat/test-find_parentage.R	New unit tests for `find_parentage()`.
R/madc2vcf_multi.R	New `madc2vcf_multi()` polyRAD-based multi-allelic conversion.
tests/testthat/test-madc2vcf_multi.R	New integration tests for `madc2vcf_multi()`.
R/check_madc_sanity.R	New MADC sanity checker + internal `check_botloci()`.
tests/testthat/test-check_madc_sanity.R	New tests for `check_madc_sanity()`.
R/get_countsMADC.R	Extended count-extraction API (`madc_object`, collapsing matches, verbose).
R/utils.R	Added `vmsg()` + `url_exists()` and updated `globalVariables()`.
R/filterVCF.R	Added `quality.rates` metrics and adjusted console output behavior.
R/check_ped.R	Reworked pedigree QC and added optional “corrected” outputs.
tests/testthat/test-check_ped.R	Updated expected output list length.
tests/testthat/test-madc2vcf_targets.R	Removed cross-function REF/ALT comparison; added large remote-file test block.
tests/testthat/test-madc2vcf_all.R	Reduced verbosity; added large remote-file test block.
tests/testthat/test-imputation_concordance.R	Minor whitespace cleanup.
R/imputation_concordance.R	Added plotting + configurable printing; updated docs.
NEWS.md	Added release notes through 0.7.0 and prior versions’ details.
DESCRIPTION	Version bump to 0.7.0; imports/suggests updated (data.table, ggplot2, polyRAD).
NAMESPACE	Exported new functions; added imports (data.table, ggplot2, etc.).
man/validate_pedigree.Rd	Generated docs for `validate_pedigree()`.
man/find_parentage.Rd	Generated docs for `find_parentage()`.
man/madc2vcf_multi.Rd	Generated docs for `madc2vcf_multi()`.
man/check_madc_sanity.Rd	Generated docs for `check_madc_sanity()`.
man/get_countsMADC.Rd	Updated docs for new `get_countsMADC()` signature.
man/get_counts.Rd	Added docs for internal `get_counts()`.
man/imputation_concordance.Rd	Updated docs for new args/behavior.
man/madc2vcf_targets.Rd	Updated docs for new args/requirements.
man/madc2vcf_all.Rd	Updated docs to reflect new required args and options.
man/filterVCF.Rd	Updated docs for `quality.rates`.
man/check_ped.Rd	Updated docs for revised `check_ped()` behavior.
man/vmsg.Rd	Added docs for `vmsg()`.
.github/workflows/R-CMD-check.yaml	CI installs polyRAD + VariantAnnotation for tests.
.gitignore	Added `.DS_Store`.
BIGr.Rproj	Added `ProjectId`.
CRAN-SUBMISSION	Removed file.
cran-comments.md	Removed file.

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

Copilot · 2026-04-06T17:53:25Z

+      (sire_vec == 0 & dam_vec == 0 & progeny_vec > 0) |
+        (sire_vec == 2 & dam_vec == 2 & progeny_vec < 2) |
+        ((sire_vec == 0 & dam_vec == 1) | (sire_vec == 1 & dam_vec == 0)) & (progeny_vec == 2) |
+        ((sire_vec == 2 & dam_vec == 1) | (sire_vec == 1 & dam_vec == 2)) & (progeny_vec == 0) |
+        ((sire_vec == 0 & dam_vec == 2) | (sire_vec == 2 & dam_vec == 0)) & (progeny_vec != 1),


The Mendelian error conditions mix | and & without grouping, so R’s operator precedence makes these tests evaluate differently than intended (e.g., A | B & C parses as A | (B & C)). This will miscount mismatches for several parent genotype combinations. Wrap each multi-part condition in parentheses so each rule is evaluated as ( (parent_combo) & (progeny_condition) ) before OR’ing the rules together.

Suggested change

(sire_vec == 0 & dam_vec == 0 & progeny_vec > 0) |

(sire_vec == 2 & dam_vec == 2 & progeny_vec < 2) |

((sire_vec == 0 & dam_vec == 1) | (sire_vec == 1 & dam_vec == 0)) & (progeny_vec == 2) |

((sire_vec == 2 & dam_vec == 1) | (sire_vec == 1 & dam_vec == 2)) & (progeny_vec == 0) |

((sire_vec == 0 & dam_vec == 2) | (sire_vec == 2 & dam_vec == 0)) & (progeny_vec != 1),

((sire_vec == 0 & dam_vec == 0 & progeny_vec > 0)) |

((sire_vec == 2 & dam_vec == 2 & progeny_vec < 2)) |

((((sire_vec == 0 & dam_vec == 1) | (sire_vec == 1 & dam_vec == 0)) & (progeny_vec == 2))) |

((((sire_vec == 2 & dam_vec == 1) | (sire_vec == 1 & dam_vec == 2)) & (progeny_vec == 0))) |

((((sire_vec == 0 & dam_vec == 2) | (sire_vec == 2 & dam_vec == 0)) & (progeny_vec != 1))),

Copilot · 2026-04-06T17:53:25Z

+        (sire_genos_mat == 0 & dam_genos_mat == 0 & progeny_vec > 0) |
+          (sire_genos_mat == 2 & dam_genos_mat == 2 & progeny_vec < 2) |
+          ((sire_genos_mat == 0 & dam_genos_mat == 1) | (sire_genos_mat == 1 & dam_genos_mat == 0)) & (progeny_vec == 2) |
+          ((sire_genos_mat == 2 & dam_genos_mat == 1) | (sire_genos_mat == 1 & dam_genos_mat == 2)) & (progeny_vec == 0) |
+          ((sire_genos_mat == 0 & dam_genos_mat == 2) | (sire_genos_mat == 2 & dam_genos_mat == 0)) & (progeny_vec != 1),


Same precedence issue as in validate_pedigree(): the Mendelian error rules combine | and & without parentheses, so the logic does not match the intended ((parent_combo) & (progeny_condition)) form and will miscount mismatches. Add explicit parentheses around each rule before combining with |.

Suggested change

(sire_genos_mat == 0 & dam_genos_mat == 0 & progeny_vec > 0) |

(sire_genos_mat == 2 & dam_genos_mat == 2 & progeny_vec < 2) |

((sire_genos_mat == 0 & dam_genos_mat == 1) | (sire_genos_mat == 1 & dam_genos_mat == 0)) & (progeny_vec == 2) |

((sire_genos_mat == 2 & dam_genos_mat == 1) | (sire_genos_mat == 1 & dam_genos_mat == 2)) & (progeny_vec == 0) |

((sire_genos_mat == 0 & dam_genos_mat == 2) | (sire_genos_mat == 2 & dam_genos_mat == 0)) & (progeny_vec != 1),

((sire_genos_mat == 0 & dam_genos_mat == 0 & progeny_vec > 0)) |

((sire_genos_mat == 2 & dam_genos_mat == 2 & progeny_vec < 2)) |

(((sire_genos_mat == 0 & dam_genos_mat == 1) | (sire_genos_mat == 1 & dam_genos_mat == 0)) & (progeny_vec == 2)) |

(((sire_genos_mat == 2 & dam_genos_mat == 1) | (sire_genos_mat == 1 & dam_genos_mat == 2)) & (progeny_vec == 0)) |

(((sire_genos_mat == 0 & dam_genos_mat == 2) | (sire_genos_mat == 2 & dam_genos_mat == 0)) & (progeny_vec != 1)),

Copilot · 2026-04-06T17:53:26Z

+
  if (!inherits(vcf.file, "vcfR")) {
-    vcf <- read.vcfR(vcf.file, verbose = FALSE)
+    vcf <- read.vcfR(vcf.file)


read.vcfR() is now called without verbose = FALSE, which can produce a lot of console output from filterVCF() even though the function has no verbosity control. Consider restoring verbose = FALSE (or adding a verbose argument to filterVCF()) to avoid noisy output in pipelines.

Suggested change

vcf <- read.vcfR(vcf.file)

vcf <- read.vcfR(vcf.file, verbose = FALSE)

Copilot · 2026-04-06T17:53:26Z

+
+    mean_depth_marker   <- rowMeans(dp_orig, na.rm = TRUE)
+    genotype_present    <- !is.na(gt_orig)
+    genotyping_rate_marker <- rowMeans(genotype_present)
+


genotype_present <- !is.na(gt_orig) treats missing genotypes like "./." as present (they are strings, not NA), which inflates genotyping-rate calculations (and downstream sample/marker stats). Treat "./." (and possibly ".|.") as missing when computing genotype_present and heterozygosity.

Copilot · 2026-04-06T17:53:26Z

  }

+  #Message that includes the output vcf stats
+  print(vcf)


print(vcf) is executed unconditionally at the end, which can be very expensive/noisy for large VCFs and cannot be disabled. Consider removing this print or guarding it behind a new verbose flag (or reuse quality.rates).

Suggested change

print(vcf)

if (isTRUE(quality.rates)) {

print(vcf)

}

Copilot · 2026-04-06T17:53:28Z

+test_that("check madc",{
+
+  github_path <- "https://raw.githubusercontent.com/Breeding-Insight/BIGapp-PanelHub/refs/heads/long_seq/test_madcs/"
+  names <- c("Columns", "FixAlleleIDs", "IUPACcodes", "LowerCase", "Indels", "ChromPos", "allNAcol", "allNArow", "RefAltSeqs", "OtherAlleles")


These tests download files from GitHub but don’t call skip_if_offline(), so they will fail in offline/CRAN/air-gapped CI environments. Add skip_if_offline("raw.githubusercontent.com") (or equivalent) near the top of the test file.

Copilot · 2026-04-06T17:53:28Z

+# CONCLUSION: We must allow heterozygous markers but avoid the
+# operator-precedence bug. Looking at the source code condition:
+#
+#   ((sire==0 & dam==1) | (sire==1 & dam==0)) & (prog==2)
+#


The test design/comments explicitly rely on a known operator-precedence bug in the Mendelian mismatch logic. Tests should validate intended behavior, not depend on buggy behavior to break ties; otherwise fixing the code will require rewriting tests. After correcting precedence in find_parentage(), update toy genotypes/expectations accordingly.

Copilot · 2026-04-06T17:53:28Z

+#' rows/columns, and sets `n.header.rows` automatically based on whether the
+#' MADC file follows the raw DArT format (6 header rows) or the fixed allele ID
+#' format (no header rows).


The docs claim n.header.rows is set automatically for raw vs fixed MADC formats, but the implementation stops when FixAlleleIDs is FALSE and always calls readDArTag(..., n.header.rows = 0L). Please update the documentation to reflect actual behavior (or implement the advertised auto-detection).

Suggested change

#' rows/columns, and sets `n.header.rows` automatically based on whether the

#' MADC file follows the raw DArT format (6 header rows) or the fixed allele ID

#' format (no header rows).

#' rows/columns, writes the corrected data to a temporary file, and then reads

#' that file with `polyRAD::readDArTag`. It does not automatically detect raw

#' DArT files with 6 header rows; inputs are handled as fixed/headerless MADC

#' data after preprocessing.

Copilot · 2026-04-06T17:53:29Z

+#' @description
+#' Performs nine quick validations on an allele report:
+#' 1) **Columns** - required columns are present (`CloneID`, `AlleleID`, `AlleleSequence`);
+#' 2) **FixAlleleIDs** - first column's first up-to-6 rows are not all blank or `"*"`
+#'    *and* both `_0001` and `_0002` appear in `AlleleID`;


Docs say “nine quick validations”, but the implementation includes an additional OtherAlleles check (and checks/messages are initialized with OtherAlleles). Update the description/list so the documented number and items match what the function returns.

Copilot · 2026-04-06T17:53:29Z

+# BIGr 0.7.0
+
+## New function `madc2vcf_multi`
+
+- New function `madc2vcf_multi` to convert a DArTag MADC file to a VCF using the polyRAD pipeline for multiallelic genotyping


The PR description focuses on adding parentage functions, but this PR also introduces/changes substantial MADC→VCF functionality (and bumps the package to 0.7.0). Please update the PR description (or split the PR) so reviewers can accurately track scope and release impact.

Modified Sire and Dam calls to male_parent and female_parent to be species agnostic. Modified the test files to accomodate the changes in functions Modified importFrom statement for thinSNP to call specific functions and resolve warnings when installing BIGr Updated package documentation

codecov · 2026-04-09T17:39:49Z

Codecov Report

❌ Patch coverage is 71.80212% with 399 lines in your changes missing coverage. Please review.
✅ Project coverage is 78.39%. Comparing base (4f30e52) to head (9824e29).

Files with missing lines	Patch %	Lines
R/madc2vcf_all.R	65.65%	113 Missing ⚠️
R/madc2vcf_targets.R	74.49%	63 Missing ⚠️
R/validate_pedigree.R	76.00%	54 Missing ⚠️
R/filterVCF.R	21.66%	47 Missing ⚠️
R/check_ped.R	56.09%	36 Missing ⚠️
R/check_madc_sanity.R	81.15%	26 Missing ⚠️
R/madc2vcf_multi.R	72.22%	25 Missing ⚠️
R/imputation_concordance.R	50.00%	18 Missing ⚠️
R/find_parentage.R	93.33%	9 Missing ⚠️
R/get_countsMADC.R	84.61%	8 Missing ⚠️

Additional details and impacted files

@@               Coverage Diff               @@
##           development      #56      +/-   ##
===============================================
- Coverage        83.05%   78.39%   -4.67%     
===============================================
  Files               19       23       +4     
  Lines             1369     2536    +1167     
===============================================
+ Hits              1137     1988     +851     
- Misses             232      548     +316

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

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

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

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

Potential fix for pull request finding

d3a4061

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

Potential fix for pull request finding

f765c7c

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

Potential fix for pull request finding

87bb1fc

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

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

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

Update R/get_countsMADC.R

e6fce19

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

Update R/check_madc_sanity.R

669ac4e

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

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

Cristianetaniguti and others added 19 commits March 31, 2026 09:56

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 17:45

Copilot started reviewing on behalf of josuechinchilla April 6, 2026 17:46 View session

Copilot AI reviewed Apr 6, 2026

View reviewed changes

josuechinchilla closed this Apr 9, 2026

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Add parentage functions#56

Add parentage functions#56
josuechinchilla wants to merge 50 commits intodevelopmentfrom
add_parentage_functions

josuechinchilla commented Apr 6, 2026

Uh oh!

Copilot AI left a comment

Uh oh!

Copilot AI Apr 6, 2026

Uh oh!

Copilot AI Apr 6, 2026

Uh oh!

Copilot AI Apr 6, 2026

Uh oh!

Copilot AI Apr 6, 2026

Uh oh!

Copilot AI Apr 6, 2026

Uh oh!

Copilot AI Apr 6, 2026

Uh oh!

Copilot AI Apr 6, 2026

Uh oh!

Copilot AI Apr 6, 2026

Uh oh!

Copilot AI Apr 6, 2026

Uh oh!

Copilot AI Apr 6, 2026

Uh oh!

codecov bot commented Apr 9, 2026

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants

	vcf <- read.vcfR(vcf.file)
	vcf <- read.vcfR(vcf.file, verbose = FALSE)

-#' rows/columns, and sets `n.header.rows` automatically based on whether the
-#' MADC file follows the raw DArT format (6 header rows) or the fixed allele ID
-#' format (no header rows).
+#' rows/columns, writes the corrected data to a temporary file, and then reads
+#' that file with `polyRAD::readDArTag`. It does not automatically detect raw
+#' DArT files with 6 header rows; inputs are handled as fixed/headerless MADC
+#' data after preprocessing.

Conversation

josuechinchilla commented Apr 6, 2026

Uh oh!

Copilot AI left a comment

Choose a reason for hiding this comment

Pull request overview

Reviewed changes

Uh oh!

Copilot AI Apr 6, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI Apr 6, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI Apr 6, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI Apr 6, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI Apr 6, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI Apr 6, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI Apr 6, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI Apr 6, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI Apr 6, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI Apr 6, 2026

Choose a reason for hiding this comment

Uh oh!

codecov bot commented Apr 9, 2026

Codecov Report

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants