class

HTS::Tabix

Inherits HTS::Bgzf < HTS::Hts < Reference < Object

Constructors

new(file_name : Path | String, mode = "r", index = "", threads = 0, build_index = false, preset = :vcf)

build_index(file_name : Path | String, index_name = "", min_shift = 0, threads = 0, verbose = true, preset = :vcf)

Build a tabix index for file_name on disk. Uses the VCF preset by default.

Supported presets are :vcf, :bed, :gff, :sam, and :psltbl.

open(file_name : Path | String, mode = "r", index = "", threads = 0, build_index = false, preset = :vcf)

open(file_name : Path | String, mode = "r", index = "", threads = 0, build_index = false, preset = :vcf, &)

build_index(index_name = "", min_shift = 0, verbose = true, preset = :vcf)

Build a tabix index for this file. Delegates to the class method.

file_name

finalize

index_loaded?

load_index(index_name = "")

mode

name2id(name : String) : Int32

Return the sequence (chromosome) ID for name, or -1 if not found.

query(chrom : String, start : Int, end_ : Int, &)

Query by chromosome name and 0-based half-open coordinates [start, end_). Yields each matching record as an Array(String) of tab-split fields.

query(region : String, &)

Query by region string using htslib's native parser. Yields each matching record as an Array(String) of tab-split fields.

seqnames

Return the list of sequence names stored in the index.