madc2vcf updates by Cristianetaniguti · Pull Request #154 · Breeding-Insight/BIGapp

Cristianetaniguti · 2026-04-02T21:18:54Z

This adapts the dosage2vcf module with the new updates on madc2vcf functions in BIGr version 0.7.0

Details:

removes the possibility to convert from dosage and counts files
add options to convert to microhaplotype VCF (via polyRAD)
add options to collapse read counts for target SNPs
add advanced options for target + off-target SNPs:
- filter tag by alignment scores
- filter multiallelic SNPs
  - adjust depth and maf thresholds
- add Other alleles
  - adjust maximum number of SNPs and presence of indels filters
Add box to display and download the log of the madc2vcf functions
Updates the help material

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Pull request overview

This PR updates BIGapp’s dosage2vcf Shiny module to align with BIGr v0.7.0 madc2vcf functionality, removing dosage/counts report conversion paths and adding new MADC conversion options (target/off-target/microhaplotypes), advanced filtering, and an in-app log display/download.

Changes:

Simplifies input formats to MADC and Dosage Matrix, and expands marker types to include microhaplotypes.
Adds “Advanced Options” modal for off-target SNP extraction and adds a Status & Log panel with log download.
Updates help material and bumps package version.

Reviewed changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 9 comments.

File	Description
`R/mod_GS.R`	Removes extraneous blank lines (no behavioral change).
`R/mod_dosage2vcf.R`	Refactors UI/server to use updated `madc2vcf_*` functions, adds advanced options + log capture/download, updates example downloads and species resources.
`inst/help_files/DArT_Report2VCF_par.Rmd`	Updates documentation to reflect new MADC workflows, requirements, and advanced options.
`DESCRIPTION`	Version bump to 1.8.0.

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Copilot · 2026-04-02T21:24:21Z

+        error = function(e) {
+          log_lines <<- c(log_lines, paste0("Error: ", conditionMessage(e), "\n"))
          shinyalert(
-            title = "Missing input!",
-            text = "Upload MADC and/or define a output file name",
+            title = "Error",
+            text = conditionMessage(e),
            size = "s",
-            closeOnEsc = TRUE,
-            closeOnClickOutside = FALSE,
-            html = TRUE,
            type = "error",
            showConfirmButton = TRUE,
            confirmButtonText = "OK",
-            confirmButtonCol = "#004192",
-            showCancelButton = FALSE,
-            animation = TRUE
+            confirmButtonCol = "#004192"
          )
        }


The conversion is wrapped in tryCatch(), but the error handler only shows an alert and does not stop the reactive (or return a failure value). That means downstream code can still mark the job complete and expose a download path even when madc2vcf_* failed. Consider returning NULL (or re-throwing) from the error handler and updating the progress bar to an error state.

Copilot · 2026-04-02T21:24:21Z

+      updateProgressBar(session = session, id = "dosage2vcf_pb", value = 100, title = "Complete!")
+      return(output_name)



After tryCatch(), the code always updates the progress bar to 100% "Complete!" and returns output_name even if conversion failed. This can lead to attempts to bgzip/download a VCF that was never created. Gate the completion/return on success (e.g., check file.exists(output_name) and return NULL on failure).

Suggested change

updateProgressBar(session = session, id = "dosage2vcf_pb", value = 100, title = "Complete!")

return(output_name)

if (file.exists(output_name)) {

updateProgressBar(session = session, id = "dosage2vcf_pb", value = 100, title = "Complete!")

return(output_name)

}

updateProgressBar(session = session, id = "dosage2vcf_pb", value = 0, title = "Conversion failed")

return(NULL)

Copilot · 2026-04-02T21:24:21Z

+      if (is.null(input$madc_file$datapath) | input$d2v_output_name == "") {
        shinyalert(
          title = "Missing input!",
-          text = "Upload Dose Report and Counts Files",
+          text = "Upload MADC and/or define a output file name",
          size = "s",


This branch shows a "Missing input" alert when output name is empty, but it doesn't stop execution (the only req() here is for madc_file). As a result, the analysis can proceed with an empty output name and produce a download filename like ".vcf.gz". Add a req(nzchar(input$d2v_output_name)) (or return(NULL)) after the alert to enforce the requirement.

Copilot · 2026-04-02T21:24:22Z

+            } else if(input$snp_type == "target"){
+              madc2vcf_targets(read_madc, output_name, get_REF_ALT = as.logical(input$ref_alt), botloci_file = botloci,
+                               markers_info = markers_info, collapse_matches_counts = input$collapse_matches_counts)
+            } else if(input$snp_type == "multiallelic"){


In the target branch, input$ref_alt is only defined when species == 'other' (UI hides it otherwise), so as.logical(input$ref_alt) becomes logical(0) for built-in species. Also, input$collapse_matches_counts from radioButtons will arrive as a string ("TRUE"/"FALSE") and is passed through uncast. Provide defaults/coercion (e.g., use TRUE/FALSE when ref_alt is NULL and wrap collapse_matches_counts with isTRUE(as.logical(...))).

Copilot · 2026-04-02T21:24:22Z

+                        "pecan" = paste0(github_path, "pecan/Pecan_unique_alignment_top48_MAS_14K_3K_f180bp.botloci"),
+                        "potato" = paste0(github_path, "potato/potato_20K_SNPset_f180bp_forDArT_3K_f180bp.botloci"),
+                        "strawberry" = paste0(github_path, "strawberry/strawberry_20K_SNPset_f180bp_forDArT_3K_f180bp.botloci"),
+                        "sweetpotato" = paste0(github_path, "sweetpotato/sweetpotato_20K_SNPset_f180bp_forDArT_3K_f180bp.botloci"),
+                        "other" = input$botloci_file$datapath)


When species == 'other', botloci is taken from input$botloci_file$datapath, but there is no server-side validation that botloci_file was actually uploaded before running. If the user clicks Convert without uploading it, botloci becomes NULL and the BIGr conversion will likely error. Add a req(input$botloci_file) (or equivalent) when input$species == 'other'.

Copilot · 2026-04-02T21:24:22Z

    content = function(file) {
-      ex <- system.file("iris_DArT_MADC.csv", package = "BIGapp")
-      file.copy(ex, file)
+      github_path <- "https://raw.githubusercontent.com/Breeding-Insight/BIGapp-PanelHub/refs/heads/long_seq/"


This downloads an example file from a moving GitHub branch reference (refs/heads/long_seq). That URL can change or disappear, breaking the app at runtime, and it also makes the feature dependent on network availability. Prefer bundling the example file in the package (inst/extdata) or pinning to a release tag/commit hash.

Suggested change

github_path <- "https://raw.githubusercontent.com/Breeding-Insight/BIGapp-PanelHub/refs/heads/long_seq/"

github_path <- "https://raw.githubusercontent.com/Breeding-Insight/BIGapp-PanelHub/<pinned-commit-hash>/"

Copilot · 2026-04-02T21:24:22Z

+      # Select species botloci
+      github_path <- "https://raw.githubusercontent.com/Breeding-Insight/BIGapp-PanelHub/refs/heads/long_seq/"
+
+      botloci <- switch(input$species,
+                        "alfalfa" = paste0(github_path, "alfalfa/20201030-BI-Alfalfa_SNPs_DArTag-probe-design_f180bp.botloci"),
+                        "blueberry" = paste0(github_path, "blueberry/20200819-BI-Blueberry_10K_SNPs_forDArT_3K_ref_alt.botloci"),


All reference resources (botloci, allele DB, markers_info) are fetched from a GitHub branch URL (refs/heads/long_seq). Using a non-pinned branch introduces a reliability risk for production use. Consider pinning to a tagged release/commit, or shipping these resources with the app and/or caching locally after first download.

Copilot · 2026-04-02T21:24:22Z

                                                   ),
-                                                   fileInput(ns("hapDB_file"), "Upload haplotype database file (fasta) (optional)"),
-                                                   sliderInput(ns("cores"), "Number of CPU Cores", min = 1, max = (availableCores() - 1), value = 1, step = 1)
+                                                   sliderInput(ns("cores"), "Number of CPU Cores", min = 1, max = (availableCores() - 1), value = 1, step = 1), br(),


sliderInput max is set to (availableCores() - 1). On single-core environments this evaluates to 0, which can make max < min and break the UI. Consider using max(1, availableCores() - 1) (or similar) to guarantee a valid range.

Suggested change

sliderInput(ns("cores"), "Number of CPU Cores", min = 1, max = (availableCores() - 1), value = 1, step = 1), br(),

sliderInput(ns("cores"), "Number of CPU Cores", min = 1, max = max(1, availableCores() - 1), value = 1, step = 1), br(),

Copilot · 2026-04-02T21:24:23Z

        shinyalert(
          title = "Missing input!",
-          text = "Upload Dose Report and Counts Files",
+          text = "Upload MADC and/or define a output file name",


Grammar nit in the alert text: "define a output file name" should be "define an output file name".

Suggested change

text = "Upload MADC and/or define a output file name",

text = "Upload MADC and/or define an output file name",

madc2vcf updates

4dbffb1

Cristianetaniguti requested review from alex-sandercock and Copilot April 2, 2026 21:18

Copilot started reviewing on behalf of Cristianetaniguti April 2, 2026 21:19 View session

Copilot AI reviewed Apr 2, 2026

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madc2vcf updates#154

madc2vcf updates#154
Cristianetaniguti wants to merge 1 commit intoGS-Amatfrom
BIGr_v0.6.7

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		updateProgressBar(session = session, id = "dosage2vcf_pb", value = 100, title = "Complete!")
		return(output_name)

	github_path <- "https://raw.githubusercontent.com/Breeding-Insight/BIGapp-PanelHub/refs/heads/long_seq/"
	github_path <- "https://raw.githubusercontent.com/Breeding-Insight/BIGapp-PanelHub/<pinned-commit-hash>/"

	sliderInput(ns("cores"), "Number of CPU Cores", min = 1, max = (availableCores() - 1), value = 1, step = 1), br(),
	sliderInput(ns("cores"), "Number of CPU Cores", min = 1, max = max(1, availableCores() - 1), value = 1, step = 1), br(),

	text = "Upload MADC and/or define a output file name",
	text = "Upload MADC and/or define an output file name",

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