class

D4::File

Inherits Reference < Object

Constructors

new(source : Source, owns_source : Bool, requested_track : String | Nil, options : ReadOptions)
Source
open(path : String | Path, *, track : String | Nil = nil, options : ReadOptions = ReadOptions.new) : File
Source
open(source : Source, *, sync_close : Bool = false, track : String | Nil = nil, options : ReadOptions = ReadOptions.new) : File
Source

Class methods

open(path : String | Path, *, track : String | Nil = nil, options : ReadOptions = ReadOptions.new, & : File -> T) : T forall T
Source
open(source : Source, *, sync_close : Bool = false, track : String | Nil = nil, options : ReadOptions = ReadOptions.new, & : File -> T) : T forall T
Source

Instance methods

aggregate(regions : Enumerable(Region), reducer : D, *, workers : Int32 = 1) forall D
Source
chromosome_size(name : String) : Int64
Source
chromosome_size?(name : String) : Int64 | Nil
Source
chromosomes
Source
close
Source
closed?
Source
coverage(region : Region, *, thresholds : Array(Int32)) : Coverage
Source
coverage_into(region : Region, thresholds : Slice(Int32), counts : Slice(Int64)) : Int64
Source
default_track
Source
each_aggregate(regions : Enumerable(Region), reducer : D, *, workers : Int32 = 1, batch_size : Int32 = 256, &) forall D
Source
each_aggregate(regions : Indexable(Region), reducer : D, *, workers : Int32 = 1, batch_size : Int32 = 256) forall D
Source
each_bin(region : Region, *, bin_size : Int, & : BinSummary -> Nil) : Nil
Source
each_bin(region : Region, *, bin_size : Int) : BinIterator
Source
each_interval(chromosome : String, start : Int = 0, stop : Int | Nil = nil, & : RawInterval -> Nil) : Nil
Source
each_interval(chromosome : String, start : Int = 0, stop : Int | Nil = nil)
Source
each_track
Source
each_track
Source
each_value(chromosome : String, start : Int = 0, stop : Int | Nil = nil, & : Int32 -> Nil) : Nil
Source
each_value(chromosome : String, start : Int = 0, stop : Int | Nil = nil)
Source
exact_histogram(region : Region, *, max_values : Int32 = 4096) : ExactHistogram
Source
has_chromosome?(name : String) : Bool
Source
histogram(region : Region, *, value_range : Range(Int32, Int32)) : Histogram
Source
histogram_into(region : Region, counts : Slice(Int64), *, value_range : Range(Int32, Int32)) : HistogramTails
Source
matrix(names : Enumerable(String)) : Matrix
Source
mean(chromosome : String, start : Int = 0, stop : Int | Nil = nil, *, index : IndexPolicy = IndexPolicy::Auto) : Float64 | Nil
Source
mean(region : Region, *, index : IndexPolicy = IndexPolicy::Auto) : Float64 | Nil
Source
metadata
Source
minmax(chromosome : String, start : Int = 0, stop : Int | Nil = nil) : Tuple(Int32, Int32) | Nil
Source
minmax(region : Region) : Tuple(Int32, Int32) | Nil
Source
options
Source
query(chromosome : String, start : Int = 0, stop : Int | Nil = nil) : Array(RawInterval)
Source
query(chromosome : String, start : Int = 0, stop : Int | Nil = nil, & : RawInterval -> Nil) : Nil
Source
query_iter(chromosome : String, start : Int = 0, stop : Int | Nil = nil)
Source
read_values_into(chromosome : String, start : Int, buffer : Slice(Int32)) : Int32
Source
sample(region : Region, *, bins : Int32 = 256) : Array(BinSummary)
Source
scaled
Source
source
Source
sum(chromosome : String, start : Int = 0, stop : Int | Nil = nil, *, index : IndexPolicy = IndexPolicy::Auto, cancelled : Proc(Bool) | Nil = nil) : Int64
Source
sum(region : Region, *, index : IndexPolicy = IndexPolicy::Auto, cancelled : Proc(Bool) | Nil = nil) : Int64
Source
sum_index_granularity
Source
summary(chromosome : String, start : Int = 0, stop : Int | Nil = nil) : Summary
Source
summary(region : Region) : Summary
Source
track(name : String) : Track
Source
track?(name : String) : Track | Nil
Source
track_names
Source
value(chromosome : String, position : Int) : Int32
Source
values(chromosome : String, start : Int = 0, stop : Int | Nil = nil) : Array(Int32)
Source
values(region : Region) : Array(Int32)
Source