Problem with tidy_genomic_data() for multiallelic datasets about radiator HOT 5 CLOSED

library(tidyverse)
#> Loading tidyverse: ggplot2
#> Loading tidyverse: tibble
#> Loading tidyverse: tidyr
#> Loading tidyverse: readr
#> Loading tidyverse: purrr
#> Loading tidyverse: dplyr
#> Warning: package 'dplyr' was built under R version 3.4.2
#> Conflicts with tidy packages ----------------------------------------------
#> filter(): dplyr, stats
#> lag():    dplyr, stats


# A tribble that captures the state of the input df at this point in the function
input <- tibble::tribble(
  ~INDIVIDUALS, ~POP_ID, ~MARKERS, ~GT_HAPLO,
  "IND1",    "POP1",  "loc1", "000000",
  "IND2",    "POP1",  "loc1", "001002",
  "IND3",    "POP1",  "loc1", "003004"
)

# This is the original bit of code - lines 303-312 (0.0.6)
input <- input %>%
  dplyr::mutate(
    GT_VCF_NUC = dplyr::if_else(
      stringi::stri_detect_fixed(
        str = GT_HAPLO, pattern = "/"),
      GT_HAPLO,
      stringi::stri_join(GT_HAPLO, GT_HAPLO, sep = "/")),
    GT_VCF_NUC = stringi::stri_replace_na(str = GT_VCF_NUC, replacement = "./.")
  ) %>%
  dplyr::select(-GT_HAPLO)

# Note that the alleles are not split. Instead the entire 6 character genotype is treated as an allele.
# Also, missing data '000000' is not converted to NA.
input
#> # A tibble: 3 x 4
#>   INDIVIDUALS POP_ID MARKERS    GT_VCF_NUC
#>         <chr>  <chr>   <chr>         <chr>
#> 1        IND1   POP1    loc1 000000/000000
#> 2        IND2   POP1    loc1 001002/001002
#> 3        IND3   POP1    loc1 003004/003004

# Reset the input
input <- tibble::tribble(
  ~INDIVIDUALS, ~POP_ID, ~MARKERS, ~GT_HAPLO,
  "IND1",    "POP1",  "loc1", "000000",
  "IND2",    "POP1",  "loc1", "001002",
  "IND3",    "POP1",  "loc1", "003004"
)

# A modification that converts missing data to NA and splits the string into the two alleles
input <- input %>%
  dplyr::mutate(
    GT_HAPLO = replace(GT_HAPLO, which(GT_HAPLO == "000000"), NA),
    GT_VCF_NUC = dplyr::if_else(
      stringi::stri_detect_fixed(
        str = GT_HAPLO, pattern = "/"),
      GT_HAPLO,
      stringi::stri_join(stringi::stri_sub(str = GT_HAPLO, from = 1, to = 3), stringi::stri_sub(str = GT_HAPLO, from = 4, to = 6), sep = "/")),
    GT_VCF_NUC = stringi::stri_replace_na(str = GT_VCF_NUC, replacement = "./.")
  ) %>%
  dplyr::select(-GT_HAPLO)

# This is the desired output, and the function performs as it should after this point
input
#> # A tibble: 3 x 4
#>   INDIVIDUALS POP_ID MARKERS GT_VCF_NUC
#>         <chr>  <chr>   <chr>      <chr>
#> 1        IND1   POP1    loc1        ./.
#> 2        IND2   POP1    loc1    001/002
#> 3        IND3   POP1    loc1    003/004