class D4::File

• D4::File
• Reference
• Object

Defined in:

d4/bins.cr
d4/file.cr
d4/matrix.cr
d4/reducers.cr
d4/scaled.cr
d4/stats.cr

Constructors

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

Class Method Summary

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

Instance Method Summary

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

Constructor Detail

Class Method Detail

Instance Method Detail