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fix chr ID #39

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Merged
alex-sandercock merged 1 commit into from
May 22, 2025
Merged

fix chr ID #39

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7 changes: 6 additions & 1 deletion R/madc2vcf_all.R
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Original file line number Diff line number Diff line change
Expand Up @@ -169,6 +169,7 @@ 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", "alignment_score_thr"))
compare_results <- parLapply(clust, updated_by_cloneID, function(x) compare(x, botloci, alignment_score_thr))
stopCluster(clust)

Expand Down Expand Up @@ -449,7 +450,11 @@ create_VCF_body <- function(csv,
vcf_body$V3 <- as.numeric(vcf_body$V3)
rownames(vcf_body) <- NULL

vcf_body$target <- paste0(sapply(strsplit(vcf_body$target, "_"),"[[", 1), "_",as.numeric(sapply(strsplit(vcf_body$target, "_"),"[[", 2)))
# Remove padding
sp <- strsplit(vcf_body$target, "_")
pos <- sapply(sp, function(x) x[length(x)])
chr <- sapply(sp, function(x) paste0(x[-length(x)], collapse = "_"))
vcf_body$target <- paste0(chr, "_",as.numeric(pos))

# Dealing with repeated positions
# discard the ones that are not the target and keep only the first if all are off-targets
Expand Down