class
Mopdepth::Reader
- Mopdepth::Reader
- Reference
- Object
Overview
An indexed BAM/CRAM coverage reader.
A Reader owns its HTS handle and is intended for serial use. Create one
Reader per concurrent worker. Call #close, or use the block form of
Reader.open, to release the native handle deterministically.
Defined in:
mopdepth/reader.crConstant Summary
-
CHECK_INTERVAL =
65536
Constructors
Class Method Summary
Instance Method Summary
- #close : Nil
- #closed? : Bool
- #coverage(chromosome : String, *, options : Options = Options.new, control : Control = Control.new) : Coverage
- #coverage(region : Region, *, options : Options = Options.new, control : Control = Control.new) : Coverage
-
#coverage_into(region : Region, values : Array(Int32), *, options : Options = Options.new, control : Control = Control.new) : Coverage
Calculates dense coverage into a reusable caller-owned array.
- #each_coverage(regions : Enumerable(Region), *, options : Options = Options.new, control : Control = Control.new, & : Coverage -> ) : Nil
- #each_coverage(*, options : Options = Options.new, control : Control = Control.new, & : Coverage -> ) : Nil
- #file_format : String
- #path : String
- #records_examined : Int64
- #target(name : String) : Target
- #targets : Array(Target)
Constructor Detail
def self.open(path : String | Path, *, reference : String | Path = "", threads : Int32 = 0) : self
#
Class Method Detail
def self.open(path : String | Path, *, reference : String | Path = "", threads : Int32 = 0, & : self -> T) : T forall T
#
Instance Method Detail
def coverage(chromosome : String, *, options : Options = Options.new, control : Control = Control.new) : Coverage
#
def coverage(region : Region, *, options : Options = Options.new, control : Control = Control.new) : Coverage
#
def coverage_into(region : Region, values : Array(Int32), *, options : Options = Options.new, control : Control = Control.new) : Coverage
#
Calculates dense coverage into a reusable caller-owned array. On return,
the array has exactly region.length values and contains no diff sentinel.
def each_coverage(regions : Enumerable(Region), *, options : Options = Options.new, control : Control = Control.new, & : Coverage -> ) : Nil
#