Madc2vcf and Pedigree functions updates

[Cristianetaniguti]

Updates on madc2vcf functions

Details:

• If verbose = TRUE, the functions output informative messages along the process
• both functions (targets and all (targets + off-targets) markers now have check_madc_sanity function implemented. It tests:
  • [Columns] If MADC has the expected columns
  • [allNArow | allNAcol] Presence of columns and rows with all NA (happens often when people open the MADC in excel before loading in R)
  • [IUPACcodes] Presence of IUPAC codes on AlleleSequence
  • [LowerCase] Presence of lower case bases on AlleleSequence
  • [Indels] Presence of Indels
  • [ChromPos] If CloneID follows the format Chr_Pos
  • [RefAltSeqs] If all Ref Allele has corresponding Alt and vice-versa
  • [OtherAlleles] If "Other" exists in the MADC AlleleID
• madc2vcf_targets doesn’t run if:
  • MADC Column names are not correct
  • Ignore Other alleles - but inform the user if they exist or not and direct them to madc2vcf_all in case they want to extract them as well
• See the table for madc2vcf_targets requirements accordingly to MADC content:

	check status	get_REF_ALT	Requires
IUPAC	TRUE	TRUE	markers_info REF/ALT
	TRUE	FALSE	-
	FALSE	TRUE	botloci or markers_info REF/ALT
	FALSE	FALSE	-
Indels	TRUE	TRUE	markers_info REF/ALT
	TRUE	FALSE	-
	FALSE	TRUE	botloci or markers_info REF/ALT
	FALSE	FALSE	-
ChromPos	TRUE	TRUE	botloci or markers_info REF/ALT
	TRUE	FALSE	-
	FALSE	TRUE	markers_info CHR/POS/REF/ALT or markers_info CHR/POS/ + botloci
	FALSE	FALSE	markers_info CHR/POS
FixAlleleIDs	TRUE	TRUE	botloci or markers_info REF/ALT
	TRUE	FALSE	-
	FALSE	TRUE	markers_info REF/ALT
	FALSE	FALSE	-

• madc2vcf_targets got a new argument: collapse_matches_counts, if TRUE, it collapses the read counts of the RefMatch to Ref and AltMatch to Alt. Default is FALSE.

Still in progress:

• Users now have the option to generate multiallelic VCF - new function madc2vcf_multi

• madc2vcf_all and madc2vcf_multi doesn’t run if:

  • MADC Column names are not correct
  • If it is raw MADC
  • If it has IUPAC codes

• See the table for madc2vcf_all and madc2vcf_multi requirements accordingly to MADC content:

	Check status	Requires
Indels	TRUE	markers_info REF/ALT/IndelPos/IndelLenght + botloci
	FALSE	botloci
ChromPos	TRUE	botloci
	FALSE	markers_info CHR/POS + botloci
RefAltSeqs	TRUE	botloci
	FALSE	botloci + microhapdb

• test scripts were added and simulated MADC files were created to test all scenarios in all madc2vcf functions. Test files are located at: https://github.com/Breeding-Insight/BIGapp-PanelHub/tree/long_seq/test_madcs
• updated version, packages Imports in DESCRIPTION and functions documentations

[Copilot]

Pull request overview

This PR enhances BIGr’s MADC→VCF conversion and pedigree utilities by adding structured verbose messaging, stronger MADC sanity validation, and new/refined arguments and documentation to support more robust input handling.

Changes:

• Added vmsg() and integrated verbose, stepwise messaging into madc2vcf_targets(), get_countsMADC(), and madc2vcf_all().
• Introduced check_madc_sanity() and integrated it into MADC→VCF workflows, plus expanded tests and roxygen docs.
• Extended APIs (madc2vcf_targets(), get_countsMADC(), madc2vcf_all(), imputation_concordance(), filterVCF(), check_ped()) with new parameters and updated manuals.

Reviewed changes

Copilot reviewed 23 out of 24 changed files in this pull request and generated 22 comments.

Show a summary per file

File	Description
tests/testthat/test-madc2vcf_targets.R	Expands MADC→VCF target tests using external PanelHub fixtures.
tests/testthat/test-check_madc_sanity.R	Adds tests for check_madc_sanity() using external fixtures.
man/vmsg.Rd	Documents new verbose message helper.
man/madc2vcf_targets.Rd	Updates targets conversion documentation for new args and behavior.
man/madc2vcf_all.Rd	Adds markers_info argument to docs.
man/imputation_concordance.Rd	Documents new plotting/printing options.
man/get_countsMADC.Rd	Updates docs for new args and behavior.
man/get_counts.Rd	Adds internal docs for new helper get_counts().
man/filterVCF.Rd	Documents new quality.rates parameter and example edits.
man/check_ped.Rd	Updates pedigree check docs to reflect new behavior/output.
man/check_madc_sanity.Rd	Documents check_madc_sanity() checks and return structure.
R/utils.R	Adds vmsg() and url_exists().
R/madc2vcf_targets.R	Refactors madc2vcf_targets() with sanity checks, markers_info support, new args, and verbose metadata header.
R/madc2vcf_all.R	Adds input validation, sanity checks, and markers_info support in validation flow.
R/imputation_concordance.R	Adds plot and print_result options and ggplot2-based plotting.
R/get_countsMADC.R	Adds madc_object, collapsing behavior, verbose messaging; introduces get_counts() helper.
R/filterVCF.R	Adds quality.rates reporting and adjusts I/O/filter logging.
R/check_ped.R	Refactors pedigree validation and introduces optional interactive/global save behavior.
R/check_madc_sanity.R	Adds new exported sanity checker and an updated check_botloci() implementation.
NEWS.md	Adds release notes for 0.6.4 and related changes.
NAMESPACE	Exports new functions and adds new imports.
DESCRIPTION	Updates authorship/copyright entry and roxygen note version.
BIGr.Rproj	Adds ProjectId.
.gitignore	Adds .DS_Store.

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[Copilot]

Multiple test_that() calls are nested inside the outer test_that("simu alfalfa", ...). testthat doesn’t reliably support nested test_that() and this can cause misreporting or skipped tests. Split the inner blocks into separate top-level test_that() calls (and share fixture setup via helper code).

[Copilot]

There is a large block of commented-out experimental code (including local file paths) kept at the end of this exported source file. This makes maintenance harder and adds noise to the package. Consider moving it to a vignette/dev note or removing it once the approach is finalized.

Suggested change

	#This is not reliable, so no longer use this shortcut to get dosage matrix
	#test2 <- vcfR2genlight(vcf)
	#####Testing custom VCF reading function######
	# Open the gzipped VCF file
	#con <- gzfile("/Users/ams866/Desktop/output.vcf", "rt")
	# Read in the entire file
	#lines <- readLines(con)
	#close(con)
	# Read in the entire file
	#lines <- readLines("/Users/ams866/Desktop/output.vcf")
	# Filter out lines that start with ##
	#filtered_lines <- lines[!grepl("^##", lines)]
	# Create a temporary file to write the filtered lines
	#temp_file <- tempfile()
	#writeLines(filtered_lines, temp_file)
	# Read in the filtered data using read.table or read.csv
	#vcf_data <- read.table(temp_file, header = TRUE, sep = "\t", comment.char = "", check.names = FALSE)
	# Clean up the temporary file
	#unlink(temp_file)
	##Extract INFO column and Filter SNPs by those values
	#Update the filtering options by the items present in the INFO column?
	# Load required library
	#library(dplyr)
	# Split INFO column into key-value pairs

[Copilot]

The roxygen examples reference ref, test, and snps, but these objects aren’t defined in the example block. This will fail during R CMD check example execution. Make the example self-contained or wrap it in \dontrun{} / \donttest{}.

[Copilot]

The Rd example calls imputation_concordance(reference_genos = ref, imputed_genos = test, ...) but ref, test, and snps are undefined in the example section. This will fail R CMD check. Provide a runnable minimal example or guard with \dontrun{} / \donttest{}.

Suggested change

	result <- imputation_concordance(
	reference_genos = ref,
	imputed_genos = test,
	snps_2_exclude = snps,
	missing_code = 5,
	verbose = TRUE,
	plot = TRUE
	)
	# Minimal example data
	ref <- data.frame(
	ID = paste0("sample", 1:3),
	snp1 = c(0, 1, 2),
	snp2 = c(2, 2, 0)
	)
	test <- data.frame(
	ID = paste0("sample", 1:3),
	snp1 = c(0, 1, 2),
	snp2 = c(2, 1, 0)
	)
	# Exclude a SNP from the concordance calculation
	snps <- "snp2"
	result <- imputation_concordance(
	reference_genos = ref,
	imputed_genos = test,
	snps_2_exclude = snps,
	missing_code = NULL,
	verbose = TRUE,
	plot = FALSE
	)

[Copilot]

ChromPos validation doesn’t match the documented Chr_Pos requirement: it currently only checks the first token starts with any letter and can yield NA when as.numeric() returns NAs (because all() over NAs yields NA). This can force downstream code into the "ChromPos invalid" path unexpectedly. Tighten the prefix check (e.g., ^chr case-insensitive) and coerce non-numeric positions to FALSE (not NA).

Suggested change

	first <- all(grepl("^[A-Za-z]", sapply(pos, "[", 1)))
	second <- suppressWarnings(all(sapply(pos, function(x) as.numeric(x[2])) > 0))
	first_tokens <- sapply(pos, "[", 1)
	second_tokens <- sapply(pos, "[", 2)
	first <- all(grepl("^chr", first_tokens, ignore.case = TRUE))
	suppressWarnings(num_pos <- as.numeric(second_tokens))
	second <- all(!is.na(num_pos) & num_pos > 0)

[Copilot]

check_ped() prompts with readline() when verbose = TRUE (the default). This will hang in non-interactive runs (CI, scripts, Shiny). Gate prompting behind interactive() and/or add an explicit argument controlling whether to prompt/save.

[Copilot]

madc still defaults to NULL, but the function now calls read.csv(madc, ...) unconditionally. If madc is omitted, this will fail with a cryptic read.csv error instead of a clear message. Add an explicit is.null(madc) check that stop()s with a helpful error before reading.