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Merged
alex-sandercock merged 3 commits into from
May 21, 2025
Merged

Development #38

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9a9ac43
bug fix
Cristianetaniguti May 21, 2025
18ad68d
solve conflict
Cristianetaniguti May 21, 2025
73ec035
Merge pull request #37 from Breeding-Insight/madc2vcf_strawberry_fix
alex-sandercock May 21, 2025
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16 changes: 8 additions & 8 deletions R/madc2vcf_all.R
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Original file line number Diff line number Diff line change
Expand Up @@ -75,7 +75,7 @@ madc2vcf_all <- function(madc = NULL,
"out_vcf= ", out_vcf, ', ',
"verbose= ", verbose,')">')

if(!is.null(madc)) report <- read.csv(madc) else stop("Please provide a MADC file")
if(!is.null(madc)) report <- read.csv(madc, check.names = FALSE) else stop("Please provide a MADC file")
if(!is.null(botloci_file)) botloci <- read.csv(botloci_file, header = F) else stop("Please provide a botloci file")
if(!is.null(hap_seq_file)) hap_seq <- read.table(hap_seq_file, header = F) else hap_seq <- NULL

Expand Down Expand Up @@ -142,12 +142,12 @@ loop_though_dartag_report <- function(report, botloci, hap_seq, n.cores=1, align
new.file <- data.frame("AlleleID" = report[,1],
"Chromosome" = NA, "SNP_position_in_Genome" = NA,
"Ref" = NA, "Alt" =NA,
"CloneID" = report[,2], report[,3:ncol(report)])
"CloneID" = report[,2], report[,3:ncol(report)], check.names = FALSE)

by_cloneID <- split.data.frame(new.file, new.file$CloneID)

clust <- makeCluster(n.cores)
#clusterExport(clust, c("hap_seq","add_ref_alt"))
#clusterExport(clust, c("hap_seq","add_ref_alt", "nsamples"))
add_ref_alt_results <- parLapply(clust, by_cloneID, function(x) add_ref_alt(x, hap_seq, nsamples, verbose = verbose))
stopCluster(clust)

Expand All @@ -169,7 +169,6 @@ loop_though_dartag_report <- function(report, botloci, hap_seq, n.cores=1, align

clust <- makeCluster(n.cores)
#clusterExport(clust, c("botloci", "compare", "nucleotideSubstitutionMatrix", "pairwiseAlignment", "DNAString", "reverseComplement"))
#clusterExport(clust, c("botloci"))
compare_results <- parLapply(clust, updated_by_cloneID, function(x) compare(x, botloci, alignment_score_thr))
stopCluster(clust)

Expand Down Expand Up @@ -209,7 +208,6 @@ loop_though_dartag_report <- function(report, botloci, hap_seq, n.cores=1, align
#'
#' @noRd
add_ref_alt <- function(one_tag, hap_seq, nsamples, verbose = TRUE) {

# Add ref and alt
cloneID <- one_tag$CloneID[1]
ref <- paste0(cloneID, "|Ref_0001")
Expand Down Expand Up @@ -281,13 +279,14 @@ add_ref_alt <- function(one_tag, hap_seq, nsamples, verbose = TRUE) {
#'
#' @noRd
compare <- function(one_tag, botloci, alignment_score_thr = 40){
#one_tag <- updated_by_cloneID[[2]]
cloneID <- one_tag$CloneID[1]
isBotLoci <- cloneID %in% botloci[,1]
# If marker is present in the botloc list, get the reverse complement sequence
if(isBotLoci) one_tag$AlleleSequence <- sapply(one_tag$AlleleSequence, function(x) as.character(reverseComplement(DNAString(x))))

chr <- sapply(strsplit(cloneID, "_"), function(x) x[-length(x)])
if(length(chr > 1)) chr <- paste(chr, collapse = "_")

# Target SNP at the position in the ID
ref_seq <- one_tag$AlleleSequence[grep("Ref_0001$",one_tag$AlleleID)]
alt_seq <- one_tag$AlleleSequence[grep("Alt_0002$",one_tag$AlleleID)]
Expand All @@ -305,9 +304,9 @@ compare <- function(one_tag, botloci, alignment_score_thr = 40){
alt_base <- substring(alt_seq, align@subject@mismatch@unlistData, align@subject@mismatch@unlistData)

# If target alternative have N, discard whole tag
if(all(alt_base %in% c("A", "T", "C", "G"))) {
# Always only one polymorphism, if there are more than one, not sure which is the target
if(all(alt_base %in% c("A", "T", "C", "G")) & length(align@pattern@mismatch@unlistData) == 1) {

# Update with new info - always only one polymorphism, if there are more than one, not sure which is the target
update_tag <- one_tag[grep("Ref_0001$",one_tag$AlleleID),]
update_tag[,2:5] <- c(chr, pos_target, ref_base, alt_base)
update_tag_temp <- one_tag[grep("Alt_0002$",one_tag$AlleleID),]
Expand Down Expand Up @@ -365,6 +364,7 @@ compare <- function(one_tag, botloci, alignment_score_thr = 40){
return(list(update_tag = NULL,
rm_score = cloneID,
rm_N = NULL))

}
}

Expand Down