search

zhengxwen / SeqArray

Data management of large-scale whole-genome sequence variant calls (Development version only)
http://www.bioconductor.org/packages/SeqArray
43 stars 12 forks source link

seqBED2GDS fails if "#" character is present in variant identifier #63

Closed smgogarten closed 4 years ago

smgogarten commented 4 years ago

I have a BIM file where one of the variant identifiers contains a comment character: HPA#_SNP1. When trying to process this file, seqBED2GDS fails with this error:

Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  : 
  line 341656 did not have 6 elements

Can you turn off comment character recognition in seqBED2GDS, or add an option to do so? Modifying this line: https://github.com/zhengxwen/SeqArray/blob/master/R/Conversion.R#L831 with comment.char="" would fix the issue.

zhengxwen commented 4 years ago

the commit 3a58ab0 fix the problem.