read_bed fails on existing file with non-.bed extension

[richelbilderbeek]

Dear genio maintainers,

genio is great!

There is something unexpected I found that I try to convince is a bit weird :-)

Usually, read_bed works awesome:

bim <- genio::read_bim(file = "demo_assoc.bim")
fam <- genio::read_fam(file = "demo_assoc.fam")
genio::read_bed(
  file = "demo_assoc.bed",
  names_loci = bim$id,
  names_ind = fam$id
)

When I copy the .bed file to a filename with another extension, I do expect read_bed to keep working:

file.copy("demo_assoc.bed", "other.ext")
genio::read_bed(
  file = "other.ext",
  names_loci = bim$id,
  names_ind = fam$id
)

Unexpectedly, it does not work:

Reading: other.ext.bed
Error in genio::read_bed(file = "other.ext", names_loci = bim$id, names_ind = fam$id) :
  File does not exist: other.ext.bed

The error message is clear: genio adds a .bed file extension unnecessarily, resulting in that file path the be absent.

I suggest to allow read_bed to also read files with a non-.bed file extension.

Here are all the input files and script I used:

genio_issue.zip

[alexviiia]

Hi Richel!
I corrected this particular issue in the latest commit. I have an internal test that replicates this scenario and confirms the solution, but of course if you're still having problems let me know.
I'm working on the next issue, may have a solution later today.
-Alex

[richelbilderbeek]

Hi @alexviiia, thanks so much!