class

D4::Track

Inherits Reference < Object

Constructors

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

Instance methods

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

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

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_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
has_index?(kind : IndexKind) : 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
materialization_limit
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
name
Source
read_values_into(chromosome : String, start : Int, buffer : Slice(Int32)) : Int32
Source
sample(region : Region, *, bins : Int32 = 256) : Array(BinSummary)
Source
scaled
Source
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. Cancellation is cooperative; an in-flight source read is allowed to finish before the next checkpoint.

Source
scan_values(region : Region, buffer : Slice(Int32), *, cancelled : Proc(Bool) | Nil = nil, & : Int64, Slice(Int32), Int32 -> Nil) : Nil
Source
secondary_table
Source
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.

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

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

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