Commit ⋅ BioJulia/GenomicFeatures.jl

# This file is a part of BioJulia.
# License is MIT: https://github.com/BioJulia/Bio.jl/blob/master/LICENSE.md

"""
# Outer constructors
* [`Strand(strand::Char)`](@ref)
* [`Strand(strand::UInt8)`](@ref)

[`Strand`](@ref) can take four kinds of values listed in the next table:

| Symbol | Constant              | Meaning                           |
| :----- | :-------------------- | :-------------------------------- |
| `'?'`  | [`STRAND_NA`](@ref)   | strand is unknown or inapplicable |
| `'+'`  | [`STRAND_POS`](@ref)  | positive strand                   |
| `'-'`  | [`STRAND_NEG`](@ref)  | negative strand                   |
| `'.'`  | [`STRAND_BOTH`](@ref) | non-strand-specific feature       |
"""
primitive type Strand 8 end

Base.convert(::Type{Strand}, strand::UInt8) = reinterpret(Strand, strand)

"""
    Strand(strand::UInt8)
"""
Strand(strand::UInt8) = convert(Strand, strand)
Base.convert(::Type{UInt8}, strand::Strand) = reinterpret(UInt8, strand)


@@ -45,6 +63,10 @@


    error("'$(strand)' is not a valid strand")
end

"""
    Strand(strand::Char)
"""
Strand(strand::Char) = convert(Strand, strand)

function Base.convert(::Type{Char}, strand::Strand)

@@ -7,7 +7,18 @@

# License is MIT: https://github.com/BioJulia/Bio.jl/blob/master/LICENSE.md

# Note, just to be clear: this shadows IntervalTrees.Interval
"A genomic interval specifies interval with some associated metadata"
"""
    struct Interval{T} <: IntervalTrees.AbstractInterval{Int64}

The first three fields (`seqname`, `first`, and `last`) are mandatory arguments when constructing the [`Interval`](@ref Interval) object.

# Fields
- `seqname::String`: the sequence name associated with the interval.
- `first::Int64`: the leftmost position.
- `last::Int64`: the rightmost position.
- `strand::Strand`: the [`strand`](@ref Strand).
- `metadata::T`
"""
struct Interval{T} <: IntervalTrees.AbstractInterval{Int64}
    seqname::String
    first::Int64

@@ -19,6 +19,23 @@

This function would return a new set of disjoint intervals with annotated coverage like:

    [1][-2-][-1-][--2--][--1--]

# Example

```jldoctest
julia> intervals = [
           Interval("chr1", 1, 8),
           Interval("chr1", 4, 20),
           Interval("chr1", 14, 27)];

julia> coverage(intervals)
IntervalCollection{UInt32} with 5 intervals:
  chr1:1-3  .  1
  chr1:4-8  .  2
  chr1:9-13  .  1
  chr1:14-20  .  2
  chr1:21-27  .  1
```
"""
function coverage(stream, seqname_isless::Function=isless)
    cov = IntervalCollection{UInt32}()

@@ -39,6 +39,7 @@

const ICTreeIntersectionIterator{F,S,T}       = IntervalTrees.IntersectionIterator{F,Int64,Interval{S},64,Interval{T},64}
const ICTreeIntervalIntersectionIterator{F,T} = IntervalTrees.IntervalIntersectionIterator{F, Int64,Interval{T},64}

"An IntervalCollection is an efficiently stored and indexed set of annotated genomic intervals."
mutable struct IntervalCollection{T}
    # Sequence name mapped to IntervalTree, which in turn maps intervals to a list of metadata.
    trees::Dict{String,ICTree{T}}

@@ -51,11 +52,12 @@

    ordered_trees::Vector{ICTree{T}}
    ordered_trees_outdated::Bool

    "Empty initaialzation."
    function IntervalCollection{T}() where T
        return new{T}(Dict{String,ICTree{T}}(), 0, ICTree{T}[], false)
    end

    # Bulk insertion.
    "Bulk insertion."
    function IntervalCollection{T}(intervals::AbstractVector{Interval{T}}, sort::Bool=false) where T
        if sort
            sort!(intervals)

@@ -80,17 +82,26 @@

    end
end

# Shorthand constructor.
"""
    IntervalCollection(intervals::AbstractVector{Interval{T}}, sort::Bool=false) where T
Shorthand constructor.
"""
function IntervalCollection(intervals::AbstractVector{Interval{T}}, sort::Bool=false) where T
    return IntervalCollection{T}(intervals, sort)
end

# Constructor that offers conversion through collection.
"""
    IntervalCollection{T}(data, sort::Bool=false) where T
Constructor that offers conversion through collection.
"""
function IntervalCollection{T}(data, sort::Bool=false) where T
    return IntervalCollection(collect(Interval{T}, data), sort)
end

# Constructor that guesses metadatatype, and offers conversion through collection.
"""
    IntervalCollection(data, sort::Bool=false)
Constructor that guesses metadatatype, and offers conversion through collection.
"""
function IntervalCollection(data, sort::Bool=false)
    return IntervalCollection(collect(Interval{metadatatype(data)}, data), sort)
end

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51	52		ordered_trees::Vector{ICTree{T}}
52	53		ordered_trees_outdated::Bool
53	54
	55	+	"Empty initaialzation."
54	56		function IntervalCollection{T}() where T
55	57		return new{T}(Dict{String,ICTree{T}}(), 0, ICTree{T}[], false)
56	58		end
57	59
58		-	# Bulk insertion.
	60	+	"Bulk insertion."
59	61		function IntervalCollection{T}(intervals::AbstractVector{Interval{T}}, sort::Bool=false) where T
60	62		if sort
61	63		sort!(intervals)

80	82		end
81	83		end
82	84
83		-	# Shorthand constructor.
	85	+	"""
	86	+	IntervalCollection(intervals::AbstractVector{Interval{T}}, sort::Bool=false) where T
	87	+	Shorthand constructor.
	88	+	"""
84	89		function IntervalCollection(intervals::AbstractVector{Interval{T}}, sort::Bool=false) where T
85	90		return IntervalCollection{T}(intervals, sort)
86	91		end
87	92
88		-	# Constructor that offers conversion through collection.
	93	+	"""
	94	+	IntervalCollection{T}(data, sort::Bool=false) where T
	95	+	Constructor that offers conversion through collection.
	96	+	"""
89	97		function IntervalCollection{T}(data, sort::Bool=false) where T
90	98		return IntervalCollection(collect(Interval{T}, data), sort)
91	99		end
92	100
93		-	# Constructor that guesses metadatatype, and offers conversion through collection.
	101	+	"""
	102	+	IntervalCollection(data, sort::Bool=false)
	103	+	Constructor that guesses metadatatype, and offers conversion through collection.
	104	+	"""
94	105		function IntervalCollection(data, sort::Bool=false)
95	106		return IntervalCollection(collect(Interval{metadatatype(data)}, data), sort)
96	107		end

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6	6		# This file is a part of BioJulia.
7	7		# License is MIT: https://github.com/BioJulia/Bio.jl/blob/master/LICENSE.md
8	8
	9	+	"""
	10	+	# Outer constructors
	11	+	* [`Strand(strand::Char)`](@ref)
	12	+	* [`Strand(strand::UInt8)`](@ref)
	13	+
	14	+	[`Strand`](@ref) can take four kinds of values listed in the next table:
	15	+
	16	+	\| Symbol \| Constant \| Meaning \|
	17	+	\| :----- \| :-------------------- \| :-------------------------------- \|
	18	+	\| `'?'` \| [`STRAND_NA`](@ref) \| strand is unknown or inapplicable \|
	19	+	\| `'+'` \| [`STRAND_POS`](@ref) \| positive strand \|
	20	+	\| `'-'` \| [`STRAND_NEG`](@ref) \| negative strand \|
	21	+	\| `'.'` \| [`STRAND_BOTH`](@ref) \| non-strand-specific feature \|
	22	+	"""
9	23		primitive type Strand 8 end
10	24
11	25		Base.convert(::Type{Strand}, strand::UInt8) = reinterpret(Strand, strand)
	26	+
	27	+	"""
	28	+	Strand(strand::UInt8)
	29	+	"""
12	30		Strand(strand::UInt8) = convert(Strand, strand)
13	31		Base.convert(::Type{UInt8}, strand::Strand) = reinterpret(UInt8, strand)
14	32

45	63
46	64		error("'$(strand)' is not a valid strand")
47	65		end
	66	+
	67	+	"""
	68	+	Strand(strand::Char)
	69	+	"""
48	70		Strand(strand::Char) = convert(Strand, strand)
49	71
50	72		function Base.convert(::Type{Char}, strand::Strand)

7	7		# License is MIT: https://github.com/BioJulia/Bio.jl/blob/master/LICENSE.md
8	8
9	9		# Note, just to be clear: this shadows IntervalTrees.Interval
10		-	"A genomic interval specifies interval with some associated metadata"
	10	+	"""
	11	+	struct Interval{T} <: IntervalTrees.AbstractInterval{Int64}
	12	+
	13	+	The first three fields (`seqname`, `first`, and `last`) are mandatory arguments when constructing the [`Interval`](@ref Interval) object.
	14	+
	15	+	# Fields
	16	+	- `seqname::String`: the sequence name associated with the interval.
	17	+	- `first::Int64`: the leftmost position.
	18	+	- `last::Int64`: the rightmost position.
	19	+	- `strand::Strand`: the [`strand`](@ref Strand).
	20	+	- `metadata::T`
	21	+	"""
11	22		struct Interval{T} <: IntervalTrees.AbstractInterval{Int64}
12	23		seqname::String
13	24		first::Int64

19	19		This function would return a new set of disjoint intervals with annotated coverage like:
20	20
21	21		[1][-2-][-1-][--2--][--1--]
	22	+
	23	+	# Example
	24	+
	25	+	```jldoctest
	26	+	julia> intervals = [
	27	+	Interval("chr1", 1, 8),
	28	+	Interval("chr1", 4, 20),
	29	+	Interval("chr1", 14, 27)];
	30	+
	31	+	julia> coverage(intervals)
	32	+	IntervalCollection{UInt32} with 5 intervals:
	33	+	chr1:1-3 . 1
	34	+	chr1:4-8 . 2
	35	+	chr1:9-13 . 1
	36	+	chr1:14-20 . 2
	37	+	chr1:21-27 . 1
	38	+	```
22	39		"""
23	40		function coverage(stream, seqname_isless::Function=isless)
24	41		cov = IntervalCollection{UInt32}()

39	39		const ICTreeIntersectionIterator{F,S,T} = IntervalTrees.IntersectionIterator{F,Int64,Interval{S},64,Interval{T},64}
40	40		const ICTreeIntervalIntersectionIterator{F,T} = IntervalTrees.IntervalIntersectionIterator{F, Int64,Interval{T},64}
41	41
	42	+	"An IntervalCollection is an efficiently stored and indexed set of annotated genomic intervals."
42	43		mutable struct IntervalCollection{T}
43	44		# Sequence name mapped to IntervalTree, which in turn maps intervals to a list of metadata.
44	45		trees::Dict{String,ICTree{T}}