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zhengxwen / SeqArray

Data management of large-scale whole-genome sequence variant calls (Development version only)
http://www.bioconductor.org/packages/SeqArray
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Duplicate indices in `seqSetFilter(f, variant.sel=)` #57

Closed zhengxwen closed 5 years ago

zhengxwen commented 5 years ago 
library(SeqArray)

# open the GDS file
f <- seqOpen(seqExampleFileName("gds"))

seqSetFilter(f, variant.sel=c(1:50, 1:50))

Fails to select the top 50 variants:

# of selected variants: 100

Incorrect read of selected variants

seqGetData(f, "chromosome")
  [1] "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1"
 [19] "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1"
 [37] "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" ""  ""  ""  ""
 [55] ""  ""  ""  ""  ""  ""  ""  ""  ""  ""  ""  ""  ""  ""  ""  ""  ""  ""
 [73] ""  ""  ""  ""  ""  ""  ""  ""  ""  ""  ""  ""  ""  ""  ""  ""  ""  ""
 [91] ""  ""  ""  ""  ""  ""  ""  ""  ""  ""