tabix.read {seqminer}

Read tabix file, similar to running tabix in command line.

Description

Read tabix file, similar to running tabix in command line.

Usage

tabix.read(tabixFile, tabixRange)

Arguments

tabixFile

character, an tabix indexed file

tabixRange

character, a text indicating which range in the VCF file to extract. e.g. 1:100-200

Value

character vector, each elements is an individual line

See Also

http://zhanxw.com/seqminer/ for online manual and examples

Examples

if (.Platform$endian == "little") {
  fileName = system.file("vcf/all.anno.filtered.extract.vcf.gz", package = "seqminer")
  snp <- tabix.read(fileName, "1:196623337-196632470")
} else {
  message("Tabix does not work well for big endian for now")
}