class

HTS::Bcf

Inherits Enumerable < HTS::Hts < Reference < Object

Constructors

new(file_name : Path | String, mode = "r", index = "", threads : Int32 = 0, build_index = false, *, subset : Enumerable(String) | Nil = nil)

Class methods

build_index(file_name : Path | String, index_name = "", min_shift = 14, threads = 0, verbose = true)

Build index for an on-disk file (callable even after close)

open(file_name : Path | String, mode = "r", index = "", threads = 0, build_index = false, *, subset : Enumerable(String) | Nil = nil)

open(file_name : Path | String, mode = "r", index = "", threads = 0, build_index = false, *, subset : Enumerable(String) | Nil = nil, &)

Instance methods

<<(var)

alt

build_index(index_name = "", min_shift = 14, verbose = true)

Instance helper delegating to the class method.

chrom

close

each(copy = false, &)

Must yield this collection's elements to the block.

each_alt

each_chrom

Do not add file-level INFO/FORMAT helpers here because these fields depend on each record and its samples. Use Bcf::Record instead.

each_endpos

each_filter

each_id

each_pos

each_qual

each_ref

endpos

file_name

filter

finalize

header

id

index_loaded?

load_index(index_name = "")

mode

nsamples

nthreads

pos

qual

query(tid : Int32, beg : Int64, end_pos : Int64, copy = false, &)

Numeric (tid) query: coordinates are 0-based half-open [beg, end)

query(chrom : String, beg : Int64, end_pos : Int64, copy = false, &)

Chromosome name + range using SAM-style 1-based inclusive coordinates.

query(region : String, copy = false, &)

query(regions : Array(String), copy = false, &)

Multi-region query. This currently uses sequential single-region iterators. It preserves the same copy semantics as the single-region query. Records overlapping multiple regions may be yielded more than once; regions are not merged or deduplicated.

ref

samples

to_a

Ensure collected records are independent and safe after iteration ends.

write(var)

write_header(header)