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Merged
alex-sandercock merged 2 commits into from
Jun 2, 2026
Merged

Update updog2vcf #63

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e2bdef5
Refactor SNP ID parsing to use regex extraction
alex-sandercock Jun 1, 2026
ef9bd78
Bump version from 0.7.0 to 0.8.0
alex-sandercock Jun 1, 2026
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
Package: BIGr
Title: Breeding Insight Genomics Functions for Polyploid and Diploid Species
Version: 0.7.0
Version: 0.8.0
Authors@R: c(person(given='Alexander M.',
family='Sandercock',
email='sandercock.alex@gmail.com',
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11 changes: 9 additions & 2 deletions R/updog2vcf.R
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Expand Up @@ -126,9 +126,16 @@ updog2vcf <- function(multidog.object, output.file, updog_version = NULL, RefAlt

#CHROM and POS from SNP ID
new_df <- mout$snpdf %>%
separate(snp, into = c("CHROM", "POS"), sep = "_") %>%
extract(
snp,
into = c("CHROM", "POS"),
regex = "^(.*)_([^_]*)$"
) %>%
Comment on lines +129 to +133
mutate(
POS = sub("^0+", "", POS),
POS = if_else(POS == "", "0", POS)
) %>%
Comment on lines +134 to +137
select(CHROM, POS)
new_df$POS <- sub("^0+", "", new_df$POS)

#Make the VCF df
vcf_df <- data.frame(
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