Comments (2)
knausb
commented on June 13, 2024
I was unsuccessful at reproducing this behavior. I have created a unit test to validate that this works. The code for this test is as follows.
library(testthat)
library(vcfR)
data(vcfR_example)
vcf2 <- vcf[grep(",", vcf@fix[,'ALT']),]
gt <- extract.gt(vcf2, element="GT", return.alleles = TRUE, allele.sep="|")
# Locus 1: 0,1,2 = T,A,G
# 0|0
expect_equal( as.character(gt[1,'BL2009P4_us23']), "T|T")
# 0|1
expect_equal( as.character(gt[1,'DDR7602']), "T|A")
# 0|2
expect_equal( as.character(gt[1,'blue13']), "T|G")
# Locus 6: 0,1,2 = G,GTCTAATAGAGGCTCGAACTC,GTCTAATAGAGGCTCGAGCTC
# 0|2
expect_equal( as.character(gt[6,'BL2009P4_us23']), "G|GTCTAATAGAGGCTCGAGCTC")
# 1|2
expect_equal( as.character(gt[6,'DDR7602']), "GTCTAATAGAGGCTCGAACTC|GTCTAATAGAGGCTCGAGCTC" )
I'll leave this open for now in case we get an example that fails.
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knausb
commented on June 13, 2024
This issue has been open for almost three months. I did not hear back from the reviewer or anyone else who could reproduce this issue. I'm therefore closing it.
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