Open bschilder opened 2 years ago
FYI, same error occurs with readvCFToMatrixByRange
target_path <- paste(
"ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20110521/",
"ALL.chr4.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz",
sep="/")
query_str <- "4:14884541-16649679"
out <- seqminer: :readvCFToMatrixByRange(fileName = target_path,
range = query_str)
seqminer::readVCFToListByRange
currently crashes Rstudio. The VCF I'm querying is definitely not missing a valid header (contrary to the error message).Moreover, even if the file was missing a header, the function should be able to handle this situation more gracefully than causing Rstudio to crash (and lose all the user's variables). Instead, a standard
stop
message should be triggered.Reprex 1
Error
Reprex 2
This imports the table successfully.
For further discussion on querying VCFs using various R packages, see here.
Session info