class D4::Track

• D4::Track
• Reference
• Object

Defined in:

d4/bins.cr
d4/reducers.cr
d4/scaled.cr
d4/stats.cr
d4/track.cr

Constructors

• .new(source : Source, directory : Format::Directory, name : String, options : ReadOptions)

Instance Method Summary

• #aggregate(regions : Enumerable(Region), reducer : D, *, workers : Int32 = 1) forall D
• #aggregate_region(region : Region, reducer : D, scratch : Slice(Int32)) forall D
• #aggregate_region(region : Region, reducer : D) forall D
• #bind_owner(owner : File) : Nil
• #check_open : Nil
• #chromosome(name : String) : Chromosome
• #chromosome?(name : String) : Chromosome | Nil
• #chromosome_size(name : String) : Int64
• #chromosome_size?(name : String) : Int64 | Nil
• #chromosomes : Array(Chromosome)
• #coverage(region : Region, *, thresholds : Array(Int32)) : Coverage
• #coverage_into(region : Region, thresholds : Slice(Int32), counts : Slice(Int64)) : Int64
• #decode_primary(chromosome : String, start : Int64, output : Slice(Int32), packed : Bytes) : Nil

  Used by the reusable scanner; callers should normally use scan_values.

• #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_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
• #has_index?(kind : IndexKind) : Bool
• #histogram(region : Region, *, value_range : Range(Int32, Int32)) : Histogram
• #histogram_into(region : Region, counts : Slice(Int64), *, value_range : Range(Int32, Int32)) : HistogramTails
• #materialization_limit : Int64
• #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
• #name : String
• #read_values_into(chromosome : String, start : Int, buffer : Slice(Int32)) : Int32
• #sample(region : Region, *, bins : Int32 = 256) : Array(BinSummary)
• #scaled : ScaledTrack
• #scan_values(chromosome : String, buffer : Slice(Int32), start : Int = 0, stop : Int | Nil = nil, *, cancelled : Proc(Bool) | Nil = nil, & : Int64, Slice(Int32), Int32 -> Nil) : Nil

  Calls cancelled at block boundaries and raises CancelledError when it returns true.

• #scan_values(region : Region, buffer : Slice(Int32), *, cancelled : Proc(Bool) | Nil = nil, & : Int64, Slice(Int32), Int32 -> Nil) : Nil
• #secondary_table : SecondaryTable | Nil
• #sum(chromosome : String, start : Int = 0, stop : Int | Nil = nil, *, index : IndexPolicy = IndexPolicy::Auto, cancelled : Proc(Bool) | Nil = nil) : Int64

  Calls cancelled between scan blocks and sum-index I/O chunks, raising CancelledError when the callback returns true.

• #sum(region : Region, *, index : IndexPolicy = IndexPolicy::Auto, cancelled : Proc(Bool) | Nil = nil) : Int64
• #sum_index_granularity : Int64 | Nil

  The number of bases represented by one sum-index block, or nil when this track has no embedded sum index.

• #summary(chromosome : String, start : Int = 0, stop : Int | Nil = nil) : Summary
• #summary(region : Region) : Summary
• #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

Instance Method Detail