mirror of
https://github.com/MillironX/XAM.jl.git
synced 2024-11-14 22:33:14 +00:00
Merge branch 'release/v0.2.5'
This commit is contained in:
Ciarán O'Mara
commit
dfa5a3217f
18 changed files with 562 additions and 609 deletions
33
.github/workflows/CompatHelper.yml
vendored
33
.github/workflows/CompatHelper.yml
vendored
|
|
@ -2,37 +2,16 @@ name: CompatHelper
|
|||
|
||||
on:
|
||||
schedule:
|
||||
- cron: '00 * * * *'
|
||||
- cron: '0 0 * * *'
|
||||
|
||||
jobs:
|
||||
CompatHelper:
|
||||
runs-on: ${{ matrix.os }}
|
||||
strategy:
|
||||
matrix:
|
||||
julia-version: [1.3.0]
|
||||
julia-arch: [x86]
|
||||
os: [ubuntu-latest]
|
||||
runs-on: ubuntu-latest
|
||||
steps:
|
||||
- uses: julia-actions/setup-julia@latest
|
||||
with:
|
||||
version: ${{ matrix.julia-version }}
|
||||
- name: Add CompatHelper
|
||||
run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
|
||||
- name: CompatHelper.main
|
||||
run: julia --color=yes -e 'using Pkg; Pkg.add("CompatHelper")'
|
||||
- name: Run CompatHelper
|
||||
env:
|
||||
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
|
||||
run: julia -e '
|
||||
using CompatHelper, Pkg;
|
||||
my_registries = [
|
||||
Pkg.RegistrySpec(
|
||||
name = "BioJuliaRegistry",
|
||||
uuid = "ccbd2cc2-2954-11e9-1ccf-f3e7900901ca",
|
||||
url = "https://github.com/BioJulia/BioJuliaRegistry.git"
|
||||
),
|
||||
Pkg.RegistrySpec(
|
||||
name = "General",
|
||||
uuid = "23338594-aafe-5451-b93e-139f81909106",
|
||||
url = "https://github.com/JuliaRegistries/General.git"
|
||||
)
|
||||
];
|
||||
CompatHelper.main(; registries = my_registries, master_branch = "master");'
|
||||
COMPATHELPER_PRIV: ${{ secrets.COMPATHELPER_PRIV }}
|
||||
run: julia --color=yes -e 'using CompatHelper; CompatHelper.main(master_branch = "master")'
|
||||
|
|
|
|||
32
.github/workflows/Documentation.yml
vendored
32
.github/workflows/Documentation.yml
vendored
|
|
@ -1,34 +1,26 @@
|
|||
name: Documentation
|
||||
name: Build Documentation
|
||||
|
||||
on:
|
||||
push:
|
||||
branches:
|
||||
- 'master'
|
||||
- 'develop'
|
||||
- 'release/.*'
|
||||
- master
|
||||
- develop
|
||||
- release/*
|
||||
tags: '*'
|
||||
pull_request:
|
||||
|
||||
jobs:
|
||||
build:
|
||||
runs-on: ${{ matrix.os }}
|
||||
strategy:
|
||||
matrix:
|
||||
julia-version: [1.3.0]
|
||||
julia-arch: [x86]
|
||||
os: [ubuntu-latest]
|
||||
runs-on: ubuntu-latest
|
||||
steps:
|
||||
- uses: actions/checkout@v1.0.0
|
||||
- uses: julia-actions/setup-julia@latest
|
||||
- uses: actions/checkout@v2
|
||||
- uses: julia-actions/setup-julia@v1
|
||||
with:
|
||||
version: ${{ matrix.julia-version }}
|
||||
- name: Install dependencies
|
||||
run: |
|
||||
julia ci_prep.jl;
|
||||
julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
|
||||
- name: Build and deploy
|
||||
version: '1'
|
||||
- name: Install Dependencies
|
||||
run: julia --color=yes --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
|
||||
- name: Build and Deploy
|
||||
env:
|
||||
# https://github.com/JuliaDocs/Documenter.jl/issues/1177
|
||||
# GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # For authentication with GitHub Actions token
|
||||
DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # For authentication with SSH deploy key
|
||||
run: julia --project=docs/ --color=yes docs/make.jl
|
||||
run: julia --color=yes --project=docs/ docs/make.jl
|
||||
|
|
|
|||
3
.github/workflows/TagBot.yml
vendored
3
.github/workflows/TagBot.yml
vendored
|
|
@ -1,7 +1,7 @@
|
|||
name: TagBot
|
||||
on:
|
||||
schedule:
|
||||
- cron: '0 * * * *'
|
||||
- cron: '0 0 * * *'
|
||||
jobs:
|
||||
TagBot:
|
||||
runs-on: ubuntu-latest
|
||||
|
|
@ -10,4 +10,3 @@ jobs:
|
|||
with:
|
||||
token: ${{ secrets.GITHUB_TOKEN }}
|
||||
ssh: ${{ secrets.TAGBOT_KEY }}
|
||||
registry: BioJulia/BioJuliaRegistry
|
||||
42
.github/workflows/UnitTests.yml
vendored
42
.github/workflows/UnitTests.yml
vendored
|
|
@ -1,22 +1,44 @@
|
|||
name: Unit tests
|
||||
name: Unit Tests
|
||||
|
||||
on: [push, pull_request]
|
||||
on:
|
||||
- push
|
||||
- pull_request
|
||||
|
||||
jobs:
|
||||
test:
|
||||
runs-on: ${{ matrix.os }}
|
||||
continue-on-error: ${{ matrix.experimental }}
|
||||
strategy:
|
||||
fail-fast: false
|
||||
matrix:
|
||||
julia-version: ['1.1', '1.2', '1.3']
|
||||
julia-arch: [x64]
|
||||
julia-version:
|
||||
- '1.0' # LTS
|
||||
- '1'
|
||||
julia-arch: [x64, x86]
|
||||
os: [ubuntu-latest, windows-latest, macOS-latest]
|
||||
experimental: [false]
|
||||
include:
|
||||
- julia-version: nightly
|
||||
julia-arch: x64
|
||||
os: ubuntu-latest
|
||||
experimental: true
|
||||
|
||||
steps:
|
||||
- uses: actions/checkout@v1.0.0
|
||||
- uses: julia-actions/setup-julia@v1
|
||||
- name: Checkout Repository
|
||||
uses: actions/checkout@v2
|
||||
- name: Setup Julia
|
||||
uses: julia-actions/setup-julia@v1
|
||||
with:
|
||||
version: ${{ matrix.julia-version }}
|
||||
arch: ${{ matrix.julia-arch }}
|
||||
- name: Install dependencies
|
||||
run: julia ci_prep.jl
|
||||
- uses: julia-actions/julia-runtest@master
|
||||
- name: Run Tests
|
||||
uses: julia-actions/julia-runtest@latest
|
||||
- name: Create CodeCov
|
||||
uses: julia-actions/julia-processcoverage@v1
|
||||
- name: Upload CodeCov
|
||||
uses: codecov/codecov-action@v1
|
||||
with:
|
||||
file: ./lcov.info
|
||||
flags: unittests
|
||||
name: codecov-umbrella
|
||||
fail_ci_if_error: false
|
||||
token: ${{ secrets.CODECOV_TOKEN }}
|
||||
|
|
|
|||
|
|
@ -1,7 +1,7 @@
|
|||
name = "XAM"
|
||||
uuid = "d759349c-bcba-11e9-07c2-5b90f8f05f7c"
|
||||
authors = ["Kenta Sato <bicycle1885@gmail.com>", "Ben J. Ward <ward9250@gmail.com>", "Ciarán O'Mara <Ciaran.OMara@utas.edu.au>"]
|
||||
version = "0.2.4"
|
||||
version = "0.2.5"
|
||||
|
||||
[deps]
|
||||
Automa = "67c07d97-cdcb-5c2c-af73-a7f9c32a568b"
|
||||
|
|
@ -19,11 +19,11 @@ Automa = "0.7, 0.8"
|
|||
BGZFStreams = "0.3"
|
||||
BioAlignments = "2"
|
||||
BioGenerics = "0.1"
|
||||
BioSequences = "2"
|
||||
BioSequences = "2.0.4"
|
||||
GenomicFeatures = "2"
|
||||
Indexes = "0.1"
|
||||
TranscodingStreams = "0.6, 0.7, 0.8, 0.9"
|
||||
julia = "1.1"
|
||||
julia = "1"
|
||||
|
||||
[extras]
|
||||
FormatSpecimens = "3372ea36-2a1a-11e9-3eb7-996970b6ffbd"
|
||||
|
|
|
|||
13
README.md
13
README.md
|
|
@ -11,18 +11,11 @@
|
|||
blog post").
|
||||
|
||||
## Description
|
||||
XAM provides I/O and utilities for manipulating SAM and BAM formatted alignment map files.
|
||||
The XAM package provides I/O and utilities for manipulating SAM and BAM formatted alignment map files.
|
||||
|
||||
## Installation
|
||||
The latest version of XAM is made available to install through BioJulia's package registry.
|
||||
By default, Julia's package manager only includes the "General" package registry.
|
||||
|
||||
To add the BioJulia registry from the [Julia REPL](https://docs.julialang.org/en/v1/manual/getting-started/), press `]` to enter [pkg mode](https://docs.julialang.org/en/v1/stdlib/Pkg/), then enter the following command:
|
||||
```julia
|
||||
registry add https://github.com/BioJulia/BioJuliaRegistry.git
|
||||
```
|
||||
|
||||
Once the registry is added to your configuration, you can install XAM while in [pkg mode](https://docs.julialang.org/en/v1/stdlib/Pkg/) with the following:
|
||||
You can install the XAM package from the [Julia REPL](https://docs.julialang.org/en/v1/manual/getting-started/).
|
||||
Press `]` to enter [pkg mode](https://docs.julialang.org/en/v1/stdlib/Pkg/), then enter the following command:
|
||||
```julia
|
||||
add XAM
|
||||
```
|
||||
|
|
|
|||
|
|
@ -1,3 +0,0 @@
|
|||
using Pkg.Registry
|
||||
Registry.add(Registry.RegistrySpec(url = "https://github.com/BioJulia/BioJuliaRegistry.git"))
|
||||
Registry.add(Registry.RegistrySpec(url = "https://github.com/JuliaRegistries/General.git"))
|
||||
|
|
@ -1,2 +0,0 @@
|
|||
[deps]
|
||||
Coverage = "a2441757-f6aa-5fb2-8edb-039e3f45d037"
|
||||
|
|
@ -1,11 +0,0 @@
|
|||
get(ENV, "TRAVIS_OS_NAME", "") == "linux" || exit()
|
||||
get(ENV, "TRAVIS_JULIA_VERSION", "") == "1.3" || exit()
|
||||
|
||||
using Pkg
|
||||
Pkg.instantiate()
|
||||
|
||||
using Coverage
|
||||
|
||||
cd(joinpath(@__DIR__, "..")) do
|
||||
Codecov.submit(Codecov.process_folder())
|
||||
end
|
||||
|
|
@ -10,20 +10,11 @@
|
|||
> This project follows the [semver](http://semver.org) pro forma and uses the [git-flow branching model](https://nvie.com/posts/a-successful-git-branching-model/).
|
||||
|
||||
## Description
|
||||
|
||||
XAM provides I/O and utilities for manipulating SAM and BAM formatted alignment map files.
|
||||
|
||||
The XAM package provides I/O and utilities for manipulating SAM and BAM formatted alignment map files.
|
||||
|
||||
## Installation
|
||||
The latest version of XAM is made available to install through BioJulia's package registry.
|
||||
By default, Julia's package manager only includes the "General" package registry.
|
||||
|
||||
To add the BioJulia registry from the [Julia REPL](https://docs.julialang.org/en/v1/manual/getting-started/), press `]` to enter [pkg mode](https://docs.julialang.org/en/v1/stdlib/Pkg/), then enter the following command:
|
||||
```julia
|
||||
registry add https://github.com/BioJulia/BioJuliaRegistry.git
|
||||
```
|
||||
|
||||
Once the registry is added to your configuration, you can install XAM while in [pkg mode](https://docs.julialang.org/en/v1/stdlib/Pkg/) with the following:
|
||||
You can install the XAM package from the [Julia REPL](https://docs.julialang.org/en/v1/manual/getting-started/).
|
||||
Press `]` to enter [pkg mode](https://docs.julialang.org/en/v1/stdlib/Pkg/), then enter the following command:
|
||||
```julia
|
||||
add XAM
|
||||
```
|
||||
|
|
|
|||
|
|
@ -287,7 +287,7 @@ SAM.Writer(IOStream(<file my-data.sam>))
|
|||
|
||||
```
|
||||
|
||||
To make a BAM Writer is slightly different, as you need to use a specific stream type from the (https://github.com/BioJulia/BGZFStreams.jl)[https://github.com/BioJulia/BGZFStreams.jl] package:
|
||||
To make a BAM Writer is slightly different, as you need to use a specific stream type from the [https://github.com/BioJulia/BGZFStreams.jl](https://github.com/BioJulia/BGZFStreams.jl) package:
|
||||
|
||||
```julia
|
||||
julia> using BGZFStreams
|
||||
|
|
|
|||
|
|
@ -48,7 +48,7 @@ Create a SAM metainfo from `str`.
|
|||
|
||||
"""
|
||||
function MetaInfo(str::AbstractString)
|
||||
return MetaInfo(Vector{UInt8}(str))
|
||||
return MetaInfo(collect(UInt8, str))
|
||||
end
|
||||
|
||||
"""
|
||||
|
|
@ -198,7 +198,7 @@ function keyvalues(metainfo::MetaInfo)::Vector{Pair{String,String}}
|
|||
if iscomment(metainfo)
|
||||
throw(ArgumentError("not a dictionary"))
|
||||
end
|
||||
return Pair{String,String}[key => val for (key, val) in zip(keys(metainfo), values(metainfo))]
|
||||
return Pair{String, String}.(keys(metainfo), values(metainfo))
|
||||
end
|
||||
|
||||
function Base.keys(metainfo::MetaInfo)
|
||||
|
|
|
|||
|
|
@ -1,12 +1,16 @@
|
|||
# Automa.jl generated readrecord! and readmetainfo! functions
|
||||
# ========================================
|
||||
|
||||
import Automa
|
||||
import Automa.RegExp: @re_str
|
||||
import Automa.Stream: @mark, @markpos, @relpos, @abspos
|
||||
|
||||
# file = header . body
|
||||
# header = metainfo*
|
||||
# body = record*
|
||||
const sam_machine_metainfo, sam_machine_record, sam_machine_header, sam_machine_body, sam_machine = (function ()
|
||||
|
||||
isinteractive() && info("compiling SAM")
|
||||
isinteractive() && @info "compiling SAM"
|
||||
|
||||
cat = Automa.RegExp.cat
|
||||
rep = Automa.RegExp.rep
|
||||
|
|
@ -161,23 +165,17 @@ function appendfrom!(dst, dpos, src, spos, n)
|
|||
if length(dst) < dpos + n - 1
|
||||
resize!(dst, dpos + n - 1)
|
||||
end
|
||||
copyto!(dst, dpos, src, spos, n)
|
||||
unsafe_copyto!(dst, dpos, src, spos, n)
|
||||
return dst
|
||||
end
|
||||
|
||||
const action_metainfo = quote
|
||||
|
||||
let markpos = @markpos()
|
||||
|
||||
appendfrom!(metainfo.data, 1, data, markpos, length(markpos:p-1))
|
||||
|
||||
metainfo.filled = @relpos(markpos):@relpos(p-1)
|
||||
appendfrom!(metainfo.data, 1, data, @markpos, p-@markpos)
|
||||
metainfo.filled = 1:(p-@markpos)
|
||||
|
||||
found_metainfo = true
|
||||
end
|
||||
|
||||
end
|
||||
|
||||
const sam_actions_metainfo = Dict(
|
||||
:mark => :(@mark),
|
||||
:pos1 => :(pos1 = @relpos(p)),
|
||||
|
|
@ -227,16 +225,12 @@ const sam_actions_record = Dict(
|
|||
:record_qual => :(record.qual = pos:@relpos(p-1)),
|
||||
:record_field => :(push!(record.fields, pos:@relpos(p-1))),
|
||||
:record => quote
|
||||
let markpos = @markpos()
|
||||
|
||||
appendfrom!(record.data, 1, data, markpos, length(markpos:p-1))
|
||||
|
||||
record.filled = @relpos(markpos):@relpos(p-1)
|
||||
appendfrom!(record.data, 1, data, @markpos, p-@markpos)
|
||||
record.filled = 1:(p-@markpos)
|
||||
|
||||
found_record = true
|
||||
@escape
|
||||
end
|
||||
end
|
||||
)
|
||||
|
||||
const sam_actions_body = merge(
|
||||
|
|
|
|||
|
|
@ -71,7 +71,7 @@ function Record(str::AbstractString)
|
|||
end
|
||||
|
||||
function Base.convert(::Type{Record}, str::AbstractString)
|
||||
return Record(Vector{UInt8}(str))
|
||||
return Record(collect(UInt8, str))
|
||||
end
|
||||
|
||||
function Base.:(==)(a::Record, b::Record)
|
||||
|
|
@ -399,7 +399,7 @@ function sequence(record::Record)::BioSequences.LongDNASeq
|
|||
end
|
||||
seqlen = length(record.seq)
|
||||
ret = BioSequences.LongDNASeq(seqlen)
|
||||
BioSequences.encode_copy!(ret, 1, record.data, first(record.seq), seqlen)
|
||||
copyto!(ret, 1, record.data, first(record.seq), seqlen)
|
||||
return ret
|
||||
end
|
||||
|
||||
|
|
|
|||
|
|
@ -5,9 +5,6 @@ module SAM
|
|||
|
||||
using BioGenerics
|
||||
|
||||
import Automa
|
||||
import Automa.RegExp: @re_str
|
||||
import Automa.Stream: @mark, @markpos, @relpos, @abspos
|
||||
import BioAlignments
|
||||
import BioGenerics: BioGenerics, isfilled, header
|
||||
import BioGenerics.Exceptions: missingerror
|
||||
|
|
|
|||
480
test/runtests.jl
480
test/runtests.jl
|
|
@ -22,482 +22,6 @@ function randrange(range)
|
|||
end
|
||||
end
|
||||
|
||||
@testset "SAM" begin
|
||||
samdir = path_of_format("SAM")
|
||||
|
||||
@testset "MetaInfo" begin
|
||||
metainfo = SAM.MetaInfo()
|
||||
@test !isfilled(metainfo)
|
||||
@test occursin("not filled", repr(metainfo))
|
||||
|
||||
metainfo = SAM.MetaInfo("CO", "some comment (parens)")
|
||||
@test isfilled(metainfo)
|
||||
@test string(metainfo) == "@CO\tsome comment (parens)"
|
||||
@test occursin("CO", repr(metainfo))
|
||||
@test SAM.tag(metainfo) == "CO"
|
||||
@test SAM.value(metainfo) == "some comment (parens)"
|
||||
@test_throws ArgumentError keys(metainfo)
|
||||
@test_throws ArgumentError values(metainfo)
|
||||
|
||||
metainfo = SAM.MetaInfo("HD", ["VN" => "1.0", "SO" => "coordinate"])
|
||||
@test isfilled(metainfo)
|
||||
@test string(metainfo) == "@HD\tVN:1.0\tSO:coordinate"
|
||||
@test occursin("HD", repr(metainfo))
|
||||
@test SAM.tag(metainfo) == "HD"
|
||||
@test SAM.value(metainfo) == "VN:1.0\tSO:coordinate"
|
||||
@test keys(metainfo) == ["VN", "SO"]
|
||||
@test values(metainfo) == ["1.0", "coordinate"]
|
||||
@test SAM.keyvalues(metainfo) == ["VN" => "1.0", "SO" => "coordinate"]
|
||||
@test haskey(metainfo, "VN")
|
||||
@test haskey(metainfo, "SO")
|
||||
@test !haskey(metainfo, "GO")
|
||||
@test metainfo["VN"] == "1.0"
|
||||
@test metainfo["SO"] == "coordinate"
|
||||
@test_throws KeyError metainfo["GO"]
|
||||
end
|
||||
|
||||
@testset "Header" begin
|
||||
header = SAM.Header()
|
||||
@test isempty(header)
|
||||
push!(header, SAM.MetaInfo("@HD\tVN:1.0\tSO:coordinate"))
|
||||
@test !isempty(header)
|
||||
@test length(header) == 1
|
||||
push!(header, SAM.MetaInfo("@CO\tsome comment"))
|
||||
@test length(header) == 2
|
||||
@test isa(collect(header), Vector{SAM.MetaInfo})
|
||||
end
|
||||
|
||||
@testset "Record" begin
|
||||
record = SAM.Record()
|
||||
@test !isfilled(record)
|
||||
@test !SAM.ismapped(record)
|
||||
@test repr(record) == "XAM.SAM.Record: <not filled>"
|
||||
@test_throws ArgumentError SAM.flag(record)
|
||||
|
||||
record = SAM.Record("r001\t99\tchr1\t7\t30\t8M2I4M1D3M\t=\t37\t39\tTTAGATAAAGGATACTG\t*")
|
||||
@test isfilled(record)
|
||||
@test occursin(r"^XAM.SAM.Record:\n", repr(record))
|
||||
@test SAM.ismapped(record)
|
||||
@test SAM.isprimary(record)
|
||||
@test SAM.hastempname(record)
|
||||
@test SAM.tempname(record) == "r001"
|
||||
@test SAM.hasflag(record)
|
||||
@test SAM.flag(record) === UInt16(99)
|
||||
@test SAM.hasrefname(record)
|
||||
@test SAM.refname(record) == "chr1"
|
||||
@test SAM.hasposition(record)
|
||||
@test SAM.position(record) === 7
|
||||
@test SAM.hasmappingquality(record)
|
||||
@test SAM.mappingquality(record) === UInt8(30)
|
||||
@test SAM.hascigar(record)
|
||||
@test SAM.cigar(record) == "8M2I4M1D3M"
|
||||
@test SAM.hasnextrefname(record)
|
||||
@test SAM.nextrefname(record) == "="
|
||||
@test SAM.hasnextposition(record)
|
||||
@test SAM.nextposition(record) === 37
|
||||
@test SAM.hastemplength(record)
|
||||
@test SAM.templength(record) === 39
|
||||
@test SAM.hassequence(record)
|
||||
@test SAM.sequence(record) == dna"TTAGATAAAGGATACTG"
|
||||
@test !SAM.hasquality(record)
|
||||
@test_throws MissingFieldException SAM.quality(record)
|
||||
end
|
||||
|
||||
@testset "Reader" begin
|
||||
reader = open(SAM.Reader, joinpath(samdir, "ce#1.sam"))
|
||||
@test isa(reader, SAM.Reader)
|
||||
@test eltype(reader) === SAM.Record
|
||||
|
||||
# header
|
||||
h = header(reader)
|
||||
@test string.(findall(header(reader), "SQ")) == ["@SQ\tSN:CHROMOSOME_I\tLN:1009800"]
|
||||
|
||||
# first record
|
||||
record = SAM.Record()
|
||||
read!(reader, record)
|
||||
@test SAM.ismapped(record)
|
||||
@test SAM.refname(record) == "CHROMOSOME_I"
|
||||
@test SAM.position(record) == leftposition(record) == 2
|
||||
@test SAM.rightposition(record) == rightposition(record) == 102
|
||||
@test SAM.tempname(record) == seqname(record) == "SRR065390.14978392"
|
||||
@test SAM.sequence(record) == sequence(record) == dna"CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA"
|
||||
@test SAM.sequence(String, record) == "CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA"
|
||||
@test SAM.seqlength(record) == 100
|
||||
@test SAM.quality(record) == (b"#############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC" .- 33)
|
||||
@test SAM.quality(String, record) == "#############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC"
|
||||
@test SAM.flag(record) == 16
|
||||
@test SAM.cigar(record) == "27M1D73M"
|
||||
@test SAM.alignment(record) == Alignment([
|
||||
AlignmentAnchor( 0, 1, OP_START),
|
||||
AlignmentAnchor( 27, 28, OP_MATCH),
|
||||
AlignmentAnchor( 27, 29, OP_DELETE),
|
||||
AlignmentAnchor(100, 102, OP_MATCH)])
|
||||
@test record["XG"] == 1
|
||||
@test record["XM"] == 5
|
||||
@test record["XN"] == 0
|
||||
@test record["XO"] == 1
|
||||
@test record["AS"] == -18
|
||||
@test record["XS"] == -18
|
||||
@test record["YT"] == "UU"
|
||||
@test eof(reader)
|
||||
close(reader)
|
||||
|
||||
# rightposition (also implicitly alignlength)
|
||||
records = collect(open(SAM.Reader, joinpath(samdir, "ce#5b.sam")))
|
||||
@test SAM.rightposition(records[6]) == rightposition(records[6]) == 83
|
||||
|
||||
# iterator
|
||||
@test length(collect(open(SAM.Reader, joinpath(samdir, "ce#1.sam")))) == 1
|
||||
@test length(collect(open(SAM.Reader, joinpath(samdir, "ce#2.sam")))) == 2
|
||||
|
||||
# IOStream
|
||||
@test length(collect(SAM.Reader(open(joinpath(samdir, "ce#1.sam"))))) == 1
|
||||
@test length(collect(SAM.Reader(open(joinpath(samdir, "ce#2.sam"))))) == 2
|
||||
end
|
||||
|
||||
@testset "Round trip" begin
|
||||
function compare_records(xs, ys)
|
||||
if length(xs) != length(ys)
|
||||
return false
|
||||
end
|
||||
for (x, y) in zip(xs, ys)
|
||||
if x.data[x.filled] != y.data[y.filled]
|
||||
return false
|
||||
end
|
||||
end
|
||||
return true
|
||||
end
|
||||
for specimen in list_valid_specimens("SAM")
|
||||
filepath = joinpath(samdir, filename(specimen))
|
||||
mktemp() do path, io
|
||||
# copy
|
||||
reader = open(SAM.Reader, filepath)
|
||||
|
||||
header_original = header(reader)
|
||||
|
||||
writer = SAM.Writer(io, header_original)
|
||||
|
||||
records = SAM.Record[]
|
||||
for record in reader
|
||||
push!(records, record)
|
||||
write(writer, record)
|
||||
end
|
||||
|
||||
close(reader)
|
||||
close(writer)
|
||||
|
||||
reader = open(SAM.Reader, path)
|
||||
|
||||
@test header(reader) == header_original
|
||||
@test compare_records(collect(reader), records)
|
||||
|
||||
close(reader)
|
||||
|
||||
end
|
||||
end
|
||||
end
|
||||
|
||||
@testset "In-Place-Reading Pattern" begin
|
||||
|
||||
file_sam = joinpath(samdir, "ce#5b.sam")
|
||||
|
||||
records = open(collect, SAM.Reader, file_sam)
|
||||
|
||||
reader = open(SAM.Reader, file_sam)
|
||||
record = SAM.Record()
|
||||
i = 0
|
||||
while !eof(reader)
|
||||
empty!(record) # Reset the record.
|
||||
read!(reader, record)
|
||||
|
||||
i = i + 1
|
||||
|
||||
@test records[i] == record
|
||||
|
||||
end
|
||||
|
||||
close(reader)
|
||||
|
||||
end
|
||||
end
|
||||
|
||||
@testset "BAM" begin
|
||||
bamdir = path_of_format("BAM")
|
||||
|
||||
@testset "AuxData" begin
|
||||
auxdata = BAM.AuxData(UInt8[])
|
||||
@test isempty(auxdata)
|
||||
|
||||
buf = IOBuffer()
|
||||
write(buf, "NM", UInt8('s'), Int16(1))
|
||||
auxdata = BAM.AuxData(take!(buf))
|
||||
@test length(auxdata) == 1
|
||||
@test auxdata["NM"] === Int16(1)
|
||||
@test collect(auxdata) == ["NM" => Int16(1)]
|
||||
|
||||
buf = IOBuffer()
|
||||
write(buf, "AS", UInt8('c'), Int8(-18))
|
||||
write(buf, "NM", UInt8('s'), Int16(1))
|
||||
write(buf, "XA", UInt8('f'), Float32(3.14))
|
||||
write(buf, "XB", UInt8('Z'), "some text\0")
|
||||
write(buf, "XC", UInt8('B'), UInt8('i'), Int32(3), Int32[10, -5, 8])
|
||||
auxdata = BAM.AuxData(take!(buf))
|
||||
@test length(auxdata) == 5
|
||||
@test auxdata["AS"] === Int8(-18)
|
||||
@test auxdata["NM"] === Int16(1)
|
||||
@test auxdata["XA"] === Float32(3.14)
|
||||
@test auxdata["XB"] == "some text"
|
||||
@test auxdata["XC"] == Int32[10, -5, 8]
|
||||
@test convert(Dict{String,Any}, auxdata) == Dict(
|
||||
"AS" => Int8(-18),
|
||||
"NM" => Int16(1),
|
||||
"XA" => Float32(3.14),
|
||||
"XB" => "some text",
|
||||
"XC" => Int32[10, -5, 8])
|
||||
end
|
||||
|
||||
@testset "Record" begin
|
||||
record = BAM.Record()
|
||||
@test !isfilled(record)
|
||||
@test repr(record) == "XAM.BAM.Record: <not filled>"
|
||||
@test_throws ArgumentError BAM.flag(record)
|
||||
end
|
||||
|
||||
@testset "Reader" begin
|
||||
reader = open(BAM.Reader, joinpath(bamdir, "ce#1.bam"))
|
||||
@test isa(reader, BAM.Reader)
|
||||
@test eltype(reader) === BAM.Record
|
||||
@test startswith(repr(reader), "XAM.BAM.Reader{IOStream}:")
|
||||
|
||||
# header
|
||||
h = header(reader)
|
||||
@test isa(h, SAM.Header)
|
||||
|
||||
# first record
|
||||
record = BAM.Record()
|
||||
read!(reader, record)
|
||||
@test BAM.ismapped(record)
|
||||
@test BAM.isprimary(record)
|
||||
@test ! BAM.ispositivestrand(record)
|
||||
@test BAM.refname(record) == "CHROMOSOME_I"
|
||||
@test BAM.refid(record) === 1
|
||||
@test BAM.hasnextrefid(record)
|
||||
@test BAM.nextrefid(record) === 0
|
||||
@test BAM.hasposition(record) === hasleftposition(record) === true
|
||||
@test BAM.position(record) === leftposition(record) === 2
|
||||
@test BAM.hasnextposition(record)
|
||||
@test BAM.nextposition(record) === 0
|
||||
@test rightposition(record) == 102
|
||||
@test BAM.hastempname(record) === hasseqname(record) === true
|
||||
@test BAM.tempname(record) == seqname(record) == "SRR065390.14978392"
|
||||
@test BAM.hassequence(record) === hassequence(record) === true
|
||||
@test BAM.sequence(record) == sequence(record) == dna"""
|
||||
CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCT
|
||||
AAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA
|
||||
"""
|
||||
@test BAM.seqlength(record) === 100
|
||||
@test BAM.hasquality(record)
|
||||
@test eltype(BAM.quality(record)) == UInt8
|
||||
@test BAM.quality(record) == [Int(x) - 33 for x in "#############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC"]
|
||||
@test BAM.flag(record) === UInt16(16)
|
||||
@test BAM.cigar(record) == "27M1D73M"
|
||||
@test BAM.alignment(record) == Alignment([
|
||||
AlignmentAnchor( 0, 1, OP_START),
|
||||
AlignmentAnchor( 27, 28, OP_MATCH),
|
||||
AlignmentAnchor( 27, 29, OP_DELETE),
|
||||
AlignmentAnchor(100, 102, OP_MATCH)])
|
||||
@test record["XG"] == 1
|
||||
@test record["XM"] == 5
|
||||
@test record["XN"] == 0
|
||||
@test record["XO"] == 1
|
||||
@test record["AS"] == -18
|
||||
@test record["XS"] == -18
|
||||
@test record["YT"] == "UU"
|
||||
@test keys(record) == ["XG","XM","XN","XO","AS","XS","YT"]
|
||||
@test values(record) == [1, 5, 0, 1, -18, -18, "UU"]
|
||||
@test eof(reader)
|
||||
close(reader)
|
||||
|
||||
# Test conversion from byte array to record
|
||||
dsize = BAM.data_size(record)
|
||||
array = Vector{UInt8}(undef, BAM.FIXED_FIELDS_BYTES + dsize)
|
||||
GC.@preserve array record begin
|
||||
ptr = Ptr{UInt8}(pointer_from_objref(record))
|
||||
unsafe_copyto!(pointer(array), ptr, BAM.FIXED_FIELDS_BYTES)
|
||||
unsafe_copyto!(array, BAM.FIXED_FIELDS_BYTES + 1, record.data, 1, dsize)
|
||||
end
|
||||
new_record = convert(BAM.Record, array)
|
||||
@test record.bin_mq_nl == new_record.bin_mq_nl
|
||||
@test record.block_size == new_record.block_size
|
||||
@test record.flag_nc == new_record.flag_nc
|
||||
@test record.l_seq == new_record.l_seq
|
||||
@test record.next_refid == new_record.next_refid
|
||||
@test record.next_pos == new_record.next_pos
|
||||
@test record.refid == new_record.refid
|
||||
@test record.pos == new_record.pos
|
||||
@test record.tlen == new_record.tlen
|
||||
@test record.data == new_record.data
|
||||
|
||||
# rightposition (also implicitly alignlength)
|
||||
records = collect(open(BAM.Reader, joinpath(bamdir, "ce#5b.bam")))
|
||||
@test BAM.rightposition(records[6]) == rightposition(records[6]) == 83
|
||||
|
||||
# iterator
|
||||
@test length(collect(open(BAM.Reader, joinpath(bamdir, "ce#1.bam")))) == 1
|
||||
@test length(collect(open(BAM.Reader, joinpath(bamdir, "ce#2.bam")))) == 2
|
||||
|
||||
# IOStream
|
||||
@test length(collect(BAM.Reader(open(joinpath(bamdir, "ce#1.bam"))))) == 1
|
||||
@test length(collect(BAM.Reader(open(joinpath(bamdir, "ce#2.bam"))))) == 2
|
||||
end
|
||||
|
||||
@testset "Read long CIGARs" begin
|
||||
function get_cigar_lens(rec::BAM.Record)
|
||||
cigar_ops, cigar_n = BAM.cigar_rle(rec)
|
||||
field_ops, field_n = BAM.cigar_rle(rec, false)
|
||||
cigar_l = length(cigar_ops)
|
||||
field_l = length(field_ops)
|
||||
return cigar_l, field_l
|
||||
end
|
||||
|
||||
function check_cigar_vs_field(rec::BAM.Record)
|
||||
cigar = BAM.cigar(rec)
|
||||
field = BAM.cigar(rec, false)
|
||||
cigar_l, field_l = get_cigar_lens(rec)
|
||||
return cigar != field && cigar_l != field_l
|
||||
end
|
||||
|
||||
function check_cigar_lens(rec::BAM.Record, field_len, cigar_len)
|
||||
cigar_l, field_l = get_cigar_lens(rec)
|
||||
return cigar_l == cigar_len && field_l == field_len
|
||||
end
|
||||
|
||||
reader = open(BAM.Reader, joinpath(bamdir, "cigar-64k.bam"))
|
||||
rec = BAM.Record()
|
||||
read!(reader, rec)
|
||||
@test !check_cigar_vs_field(rec)
|
||||
read!(reader, rec)
|
||||
@test check_cigar_vs_field(rec)
|
||||
@test check_cigar_lens(rec, 2, 72091)
|
||||
end
|
||||
|
||||
function compare_records(xs, ys)
|
||||
if length(xs) != length(ys)
|
||||
return false
|
||||
end
|
||||
for (x, y) in zip(xs, ys)
|
||||
if !(
|
||||
x.block_size == y.block_size &&
|
||||
x.refid == y.refid &&
|
||||
x.pos == y.pos &&
|
||||
x.bin_mq_nl == y.bin_mq_nl &&
|
||||
x.flag_nc == y.flag_nc &&
|
||||
x.l_seq == y.l_seq &&
|
||||
x.next_refid == y.next_refid &&
|
||||
x.next_pos == y.next_pos &&
|
||||
x.tlen == y.tlen &&
|
||||
x.data[1:BAM.data_size(x)] == y.data[1:BAM.data_size(y)])
|
||||
return false
|
||||
end
|
||||
end
|
||||
return true
|
||||
end
|
||||
|
||||
@testset "Round trip" begin
|
||||
for specimen in list_valid_specimens("BAM")
|
||||
filepath = joinpath(bamdir, filename(specimen))
|
||||
mktemp() do path, _
|
||||
# copy
|
||||
if hastags(specimen) && in("bai", tags(specimen))
|
||||
reader = open(BAM.Reader, filepath, index=filepath * ".bai")
|
||||
else
|
||||
reader = open(BAM.Reader, filepath)
|
||||
end
|
||||
|
||||
header_original = header(reader)
|
||||
|
||||
writer = BAM.Writer(BGZFStream(path, "w"), BAM.header(reader, fillSQ=isempty(findall(header(reader), "SQ"))))
|
||||
|
||||
records = BAM.Record[]
|
||||
for record in reader
|
||||
push!(records, record)
|
||||
write(writer, record)
|
||||
end
|
||||
close(reader)
|
||||
close(writer)
|
||||
|
||||
reader = open(BAM.Reader, path)
|
||||
|
||||
@test header(reader) == header_original
|
||||
@test compare_records(collect(reader), records)
|
||||
|
||||
close(reader)
|
||||
|
||||
end
|
||||
end
|
||||
end
|
||||
|
||||
@testset "In-Place-Reading Pattern" begin
|
||||
|
||||
file_bam = joinpath(bamdir, "ce#5b.bam")
|
||||
|
||||
records = open(collect, BAM.Reader, file_bam)
|
||||
|
||||
reader = open(BAM.Reader, file_bam)
|
||||
record = BAM.Record()
|
||||
i = 0
|
||||
while !eof(reader)
|
||||
empty!(record) # Reset the record.
|
||||
read!(reader, record)
|
||||
|
||||
i = i + 1
|
||||
@test records[i] == record
|
||||
end
|
||||
|
||||
close(reader)
|
||||
|
||||
end
|
||||
|
||||
@testset "Random access" begin
|
||||
filepath = joinpath(bamdir, "GSE25840_GSM424320_GM06985_gencode_spliced.head.bam")
|
||||
reader = open(BAM.Reader, filepath, index=filepath * ".bai")
|
||||
|
||||
@test isa(eachoverlap(reader, "chr1", 1:100), BAM.OverlapIterator)
|
||||
@test isa(eachoverlap(reader, GenomicFeatures.Interval("chr1", 1, 100)), BAM.OverlapIterator)
|
||||
|
||||
# expected values are counted using samtools
|
||||
for (refname, interval, expected) in [
|
||||
("chr1", 1_000:10000, 21),
|
||||
("chr1", 8_000:10000, 20),
|
||||
("chr1", 766_000:800_000, 142),
|
||||
("chr1", 786_000:800_000, 1),
|
||||
("chr1", 796_000:800_000, 0)]
|
||||
intsect = eachoverlap(reader, refname, interval)
|
||||
@test eltype(intsect) == BAM.Record
|
||||
@test count(_ -> true, intsect) == expected
|
||||
# check that the intersection iterator is stateless
|
||||
@test count(_ -> true, intsect) == expected
|
||||
end
|
||||
|
||||
# randomized tests
|
||||
for n in 1:50
|
||||
refindex = 1
|
||||
refname = "chr1"
|
||||
range = randrange(1:1_000_000)
|
||||
seekstart(reader)
|
||||
# linear scan
|
||||
expected = filter(collect(reader)) do record
|
||||
BAM.compare_intervals(record, (refindex, range)) == 0
|
||||
end
|
||||
# indexed scan
|
||||
actual = collect(eachoverlap(reader, refname, range))
|
||||
@test compare_records(actual, expected)
|
||||
end
|
||||
close(reader)
|
||||
|
||||
filepath = joinpath(bamdir, "R_12h_D06.uniq.q40.bam")
|
||||
reader = open(BAM.Reader, filepath, index=filepath * ".bai")
|
||||
@test isempty(collect(eachoverlap(reader, "chr19", 5823708:5846478)))
|
||||
close(reader)
|
||||
end
|
||||
end
|
||||
include("test_sam.jl")
|
||||
include("test_bam.jl")
|
||||
|
|
|
|||
280
test/test_bam.jl
Normal file
280
test/test_bam.jl
Normal file
|
|
@ -0,0 +1,280 @@
|
|||
@testset "BAM" begin
|
||||
bamdir = path_of_format("BAM")
|
||||
|
||||
@testset "AuxData" begin
|
||||
auxdata = BAM.AuxData(UInt8[])
|
||||
@test isempty(auxdata)
|
||||
|
||||
buf = IOBuffer()
|
||||
write(buf, "NM", UInt8('s'), Int16(1))
|
||||
auxdata = BAM.AuxData(take!(buf))
|
||||
@test length(auxdata) == 1
|
||||
@test auxdata["NM"] === Int16(1)
|
||||
@test collect(auxdata) == ["NM" => Int16(1)]
|
||||
|
||||
buf = IOBuffer()
|
||||
write(buf, "AS", UInt8('c'), Int8(-18))
|
||||
write(buf, "NM", UInt8('s'), Int16(1))
|
||||
write(buf, "XA", UInt8('f'), Float32(3.14))
|
||||
write(buf, "XB", UInt8('Z'), "some text\0")
|
||||
write(buf, "XC", UInt8('B'), UInt8('i'), Int32(3), Int32[10, -5, 8])
|
||||
auxdata = BAM.AuxData(take!(buf))
|
||||
@test length(auxdata) == 5
|
||||
@test auxdata["AS"] === Int8(-18)
|
||||
@test auxdata["NM"] === Int16(1)
|
||||
@test auxdata["XA"] === Float32(3.14)
|
||||
@test auxdata["XB"] == "some text"
|
||||
@test auxdata["XC"] == Int32[10, -5, 8]
|
||||
@test convert(Dict{String,Any}, auxdata) == Dict(
|
||||
"AS" => Int8(-18),
|
||||
"NM" => Int16(1),
|
||||
"XA" => Float32(3.14),
|
||||
"XB" => "some text",
|
||||
"XC" => Int32[10, -5, 8])
|
||||
end
|
||||
|
||||
@testset "Record" begin
|
||||
record = BAM.Record()
|
||||
@test !isfilled(record)
|
||||
@test repr(record) == "XAM.BAM.Record: <not filled>"
|
||||
@test_throws ArgumentError BAM.flag(record)
|
||||
end
|
||||
|
||||
@testset "Reader" begin
|
||||
reader = open(BAM.Reader, joinpath(bamdir, "ce#1.bam"))
|
||||
@test isa(reader, BAM.Reader)
|
||||
@test eltype(reader) === BAM.Record
|
||||
@test startswith(repr(reader), "XAM.BAM.Reader{IOStream}:")
|
||||
|
||||
# header
|
||||
h = header(reader)
|
||||
@test isa(h, SAM.Header)
|
||||
|
||||
# first record
|
||||
record = BAM.Record()
|
||||
read!(reader, record)
|
||||
@test BAM.ismapped(record)
|
||||
@test BAM.isprimary(record)
|
||||
@test ! BAM.ispositivestrand(record)
|
||||
@test BAM.refname(record) == "CHROMOSOME_I"
|
||||
@test BAM.refid(record) === 1
|
||||
@test BAM.hasnextrefid(record)
|
||||
@test BAM.nextrefid(record) === 0
|
||||
@test BAM.hasposition(record) === hasleftposition(record) === true
|
||||
@test BAM.position(record) === leftposition(record) === 2
|
||||
@test BAM.hasnextposition(record)
|
||||
@test BAM.nextposition(record) === 0
|
||||
@test rightposition(record) == 102
|
||||
@test BAM.hastempname(record) === hasseqname(record) === true
|
||||
@test BAM.tempname(record) == seqname(record) == "SRR065390.14978392"
|
||||
@test BAM.hassequence(record) === hassequence(record) === true
|
||||
@test BAM.sequence(record) == sequence(record) == dna"""
|
||||
CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCT
|
||||
AAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA
|
||||
"""
|
||||
@test BAM.seqlength(record) === 100
|
||||
@test BAM.hasquality(record)
|
||||
@test eltype(BAM.quality(record)) == UInt8
|
||||
@test BAM.quality(record) == [Int(x) - 33 for x in "#############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC"]
|
||||
@test BAM.flag(record) === UInt16(16)
|
||||
@test BAM.cigar(record) == "27M1D73M"
|
||||
@test BAM.alignment(record) == Alignment([
|
||||
AlignmentAnchor( 0, 1, OP_START),
|
||||
AlignmentAnchor( 27, 28, OP_MATCH),
|
||||
AlignmentAnchor( 27, 29, OP_DELETE),
|
||||
AlignmentAnchor(100, 102, OP_MATCH)])
|
||||
@test record["XG"] == 1
|
||||
@test record["XM"] == 5
|
||||
@test record["XN"] == 0
|
||||
@test record["XO"] == 1
|
||||
@test record["AS"] == -18
|
||||
@test record["XS"] == -18
|
||||
@test record["YT"] == "UU"
|
||||
@test keys(record) == ["XG","XM","XN","XO","AS","XS","YT"]
|
||||
@test values(record) == [1, 5, 0, 1, -18, -18, "UU"]
|
||||
@test eof(reader)
|
||||
close(reader)
|
||||
|
||||
# Test conversion from byte array to record
|
||||
dsize = BAM.data_size(record)
|
||||
array = Vector{UInt8}(undef, BAM.FIXED_FIELDS_BYTES + dsize)
|
||||
GC.@preserve array record begin
|
||||
ptr = Ptr{UInt8}(pointer_from_objref(record))
|
||||
unsafe_copyto!(pointer(array), ptr, BAM.FIXED_FIELDS_BYTES)
|
||||
unsafe_copyto!(array, BAM.FIXED_FIELDS_BYTES + 1, record.data, 1, dsize)
|
||||
end
|
||||
new_record = convert(BAM.Record, array)
|
||||
@test record.bin_mq_nl == new_record.bin_mq_nl
|
||||
@test record.block_size == new_record.block_size
|
||||
@test record.flag_nc == new_record.flag_nc
|
||||
@test record.l_seq == new_record.l_seq
|
||||
@test record.next_refid == new_record.next_refid
|
||||
@test record.next_pos == new_record.next_pos
|
||||
@test record.refid == new_record.refid
|
||||
@test record.pos == new_record.pos
|
||||
@test record.tlen == new_record.tlen
|
||||
@test record.data == new_record.data
|
||||
|
||||
# rightposition (also implicitly alignlength)
|
||||
records = collect(open(BAM.Reader, joinpath(bamdir, "ce#5b.bam")))
|
||||
@test BAM.rightposition(records[6]) == rightposition(records[6]) == 83
|
||||
|
||||
# iterator
|
||||
@test length(collect(open(BAM.Reader, joinpath(bamdir, "ce#1.bam")))) == 1
|
||||
@test length(collect(open(BAM.Reader, joinpath(bamdir, "ce#2.bam")))) == 2
|
||||
|
||||
# IOStream
|
||||
@test length(collect(BAM.Reader(open(joinpath(bamdir, "ce#1.bam"))))) == 1
|
||||
@test length(collect(BAM.Reader(open(joinpath(bamdir, "ce#2.bam"))))) == 2
|
||||
end
|
||||
|
||||
@testset "Read long CIGARs" begin
|
||||
function get_cigar_lens(rec::BAM.Record)
|
||||
cigar_ops, cigar_n = BAM.cigar_rle(rec)
|
||||
field_ops, field_n = BAM.cigar_rle(rec, false)
|
||||
cigar_l = length(cigar_ops)
|
||||
field_l = length(field_ops)
|
||||
return cigar_l, field_l
|
||||
end
|
||||
|
||||
function check_cigar_vs_field(rec::BAM.Record)
|
||||
cigar = BAM.cigar(rec)
|
||||
field = BAM.cigar(rec, false)
|
||||
cigar_l, field_l = get_cigar_lens(rec)
|
||||
return cigar != field && cigar_l != field_l
|
||||
end
|
||||
|
||||
function check_cigar_lens(rec::BAM.Record, field_len, cigar_len)
|
||||
cigar_l, field_l = get_cigar_lens(rec)
|
||||
return cigar_l == cigar_len && field_l == field_len
|
||||
end
|
||||
|
||||
reader = open(BAM.Reader, joinpath(bamdir, "cigar-64k.bam"))
|
||||
rec = BAM.Record()
|
||||
read!(reader, rec)
|
||||
@test !check_cigar_vs_field(rec)
|
||||
read!(reader, rec)
|
||||
@test check_cigar_vs_field(rec)
|
||||
@test check_cigar_lens(rec, 2, 72091)
|
||||
end
|
||||
|
||||
function compare_records(xs, ys)
|
||||
if length(xs) != length(ys)
|
||||
return false
|
||||
end
|
||||
for (x, y) in zip(xs, ys)
|
||||
if !(
|
||||
x.block_size == y.block_size &&
|
||||
x.refid == y.refid &&
|
||||
x.pos == y.pos &&
|
||||
x.bin_mq_nl == y.bin_mq_nl &&
|
||||
x.flag_nc == y.flag_nc &&
|
||||
x.l_seq == y.l_seq &&
|
||||
x.next_refid == y.next_refid &&
|
||||
x.next_pos == y.next_pos &&
|
||||
x.tlen == y.tlen &&
|
||||
x.data[1:BAM.data_size(x)] == y.data[1:BAM.data_size(y)])
|
||||
return false
|
||||
end
|
||||
end
|
||||
return true
|
||||
end
|
||||
|
||||
@testset "Round trip" begin
|
||||
for specimen in list_valid_specimens("BAM")
|
||||
filepath = joinpath(bamdir, filename(specimen))
|
||||
mktemp() do path, _
|
||||
# copy
|
||||
if hastags(specimen) && in("bai", tags(specimen))
|
||||
reader = open(BAM.Reader, filepath, index=filepath * ".bai")
|
||||
else
|
||||
reader = open(BAM.Reader, filepath)
|
||||
end
|
||||
|
||||
header_original = header(reader)
|
||||
|
||||
writer = BAM.Writer(BGZFStream(path, "w"), BAM.header(reader, fillSQ=isempty(findall(header(reader), "SQ"))))
|
||||
|
||||
records = BAM.Record[]
|
||||
for record in reader
|
||||
push!(records, record)
|
||||
write(writer, record)
|
||||
end
|
||||
close(reader)
|
||||
close(writer)
|
||||
|
||||
reader = open(BAM.Reader, path)
|
||||
|
||||
@test header(reader) == header_original
|
||||
@test compare_records(collect(reader), records)
|
||||
|
||||
close(reader)
|
||||
|
||||
end
|
||||
end
|
||||
end
|
||||
|
||||
@testset "In-Place-Reading Pattern" begin
|
||||
|
||||
file_bam = joinpath(bamdir, "ce#5b.bam")
|
||||
|
||||
records = open(collect, BAM.Reader, file_bam)
|
||||
|
||||
reader = open(BAM.Reader, file_bam)
|
||||
record = BAM.Record()
|
||||
i = 0
|
||||
while !eof(reader)
|
||||
empty!(record) # Reset the record.
|
||||
read!(reader, record)
|
||||
|
||||
i = i + 1
|
||||
@test records[i] == record
|
||||
end
|
||||
|
||||
close(reader)
|
||||
|
||||
end
|
||||
|
||||
@testset "Random access" begin
|
||||
filepath = joinpath(bamdir, "GSE25840_GSM424320_GM06985_gencode_spliced.head.bam")
|
||||
reader = open(BAM.Reader, filepath, index=filepath * ".bai")
|
||||
|
||||
@test isa(eachoverlap(reader, "chr1", 1:100), BAM.OverlapIterator)
|
||||
@test isa(eachoverlap(reader, GenomicFeatures.Interval("chr1", 1, 100)), BAM.OverlapIterator)
|
||||
|
||||
# expected values are counted using samtools
|
||||
for (refname, interval, expected) in [
|
||||
("chr1", 1_000:10000, 21),
|
||||
("chr1", 8_000:10000, 20),
|
||||
("chr1", 766_000:800_000, 142),
|
||||
("chr1", 786_000:800_000, 1),
|
||||
("chr1", 796_000:800_000, 0)]
|
||||
intsect = eachoverlap(reader, refname, interval)
|
||||
@test eltype(intsect) == BAM.Record
|
||||
@test count(_ -> true, intsect) == expected
|
||||
# check that the intersection iterator is stateless
|
||||
@test count(_ -> true, intsect) == expected
|
||||
end
|
||||
|
||||
# randomized tests
|
||||
for n in 1:50
|
||||
refindex = 1
|
||||
refname = "chr1"
|
||||
range = randrange(1:1_000_000)
|
||||
seekstart(reader)
|
||||
# linear scan
|
||||
expected = filter(collect(reader)) do record
|
||||
BAM.compare_intervals(record, (refindex, range)) == 0
|
||||
end
|
||||
# indexed scan
|
||||
actual = collect(eachoverlap(reader, refname, range))
|
||||
@test compare_records(actual, expected)
|
||||
end
|
||||
close(reader)
|
||||
|
||||
filepath = joinpath(bamdir, "R_12h_D06.uniq.q40.bam")
|
||||
reader = open(BAM.Reader, filepath, index=filepath * ".bai")
|
||||
@test isempty(collect(eachoverlap(reader, "chr19", 5823708:5846478)))
|
||||
close(reader)
|
||||
end
|
||||
end
|
||||
198
test/test_sam.jl
Normal file
198
test/test_sam.jl
Normal file
|
|
@ -0,0 +1,198 @@
|
|||
@testset "SAM" begin
|
||||
samdir = path_of_format("SAM")
|
||||
|
||||
@testset "MetaInfo" begin
|
||||
metainfo = SAM.MetaInfo()
|
||||
@test !isfilled(metainfo)
|
||||
@test occursin("not filled", repr(metainfo))
|
||||
|
||||
metainfo = SAM.MetaInfo("CO", "some comment (parens)")
|
||||
@test isfilled(metainfo)
|
||||
@test string(metainfo) == "@CO\tsome comment (parens)"
|
||||
@test occursin("CO", repr(metainfo))
|
||||
@test SAM.tag(metainfo) == "CO"
|
||||
@test SAM.value(metainfo) == "some comment (parens)"
|
||||
@test_throws ArgumentError keys(metainfo)
|
||||
@test_throws ArgumentError values(metainfo)
|
||||
|
||||
metainfo = SAM.MetaInfo("HD", ["VN" => "1.0", "SO" => "coordinate"])
|
||||
@test isfilled(metainfo)
|
||||
@test string(metainfo) == "@HD\tVN:1.0\tSO:coordinate"
|
||||
@test occursin("HD", repr(metainfo))
|
||||
@test SAM.tag(metainfo) == "HD"
|
||||
@test SAM.value(metainfo) == "VN:1.0\tSO:coordinate"
|
||||
@test keys(metainfo) == ["VN", "SO"]
|
||||
@test values(metainfo) == ["1.0", "coordinate"]
|
||||
@test SAM.keyvalues(metainfo) == ["VN" => "1.0", "SO" => "coordinate"]
|
||||
@test haskey(metainfo, "VN")
|
||||
@test haskey(metainfo, "SO")
|
||||
@test !haskey(metainfo, "GO")
|
||||
@test metainfo["VN"] == "1.0"
|
||||
@test metainfo["SO"] == "coordinate"
|
||||
@test_throws KeyError metainfo["GO"]
|
||||
end
|
||||
|
||||
@testset "Header" begin
|
||||
header = SAM.Header()
|
||||
@test isempty(header)
|
||||
push!(header, SAM.MetaInfo("@HD\tVN:1.0\tSO:coordinate"))
|
||||
@test !isempty(header)
|
||||
@test length(header) == 1
|
||||
push!(header, SAM.MetaInfo("@CO\tsome comment"))
|
||||
@test length(header) == 2
|
||||
@test isa(collect(header), Vector{SAM.MetaInfo})
|
||||
end
|
||||
|
||||
@testset "Record" begin
|
||||
record = SAM.Record()
|
||||
@test !isfilled(record)
|
||||
@test !SAM.ismapped(record)
|
||||
@test repr(record) == "XAM.SAM.Record: <not filled>"
|
||||
@test_throws ArgumentError SAM.flag(record)
|
||||
|
||||
record = SAM.Record("r001\t99\tchr1\t7\t30\t8M2I4M1D3M\t=\t37\t39\tTTAGATAAAGGATACTG\t*")
|
||||
@test isfilled(record)
|
||||
@test occursin(r"^XAM.SAM.Record:\n", repr(record))
|
||||
@test SAM.ismapped(record)
|
||||
@test SAM.isprimary(record)
|
||||
@test SAM.hastempname(record)
|
||||
@test SAM.tempname(record) == "r001"
|
||||
@test SAM.hasflag(record)
|
||||
@test SAM.flag(record) === UInt16(99)
|
||||
@test SAM.hasrefname(record)
|
||||
@test SAM.refname(record) == "chr1"
|
||||
@test SAM.hasposition(record)
|
||||
@test SAM.position(record) === 7
|
||||
@test SAM.hasmappingquality(record)
|
||||
@test SAM.mappingquality(record) === UInt8(30)
|
||||
@test SAM.hascigar(record)
|
||||
@test SAM.cigar(record) == "8M2I4M1D3M"
|
||||
@test SAM.hasnextrefname(record)
|
||||
@test SAM.nextrefname(record) == "="
|
||||
@test SAM.hasnextposition(record)
|
||||
@test SAM.nextposition(record) === 37
|
||||
@test SAM.hastemplength(record)
|
||||
@test SAM.templength(record) === 39
|
||||
@test SAM.hassequence(record)
|
||||
@test SAM.sequence(record) == dna"TTAGATAAAGGATACTG"
|
||||
@test !SAM.hasquality(record)
|
||||
@test_throws MissingFieldException SAM.quality(record)
|
||||
end
|
||||
|
||||
@testset "Reader" begin
|
||||
reader = open(SAM.Reader, joinpath(samdir, "ce#1.sam"))
|
||||
@test isa(reader, SAM.Reader)
|
||||
@test eltype(reader) === SAM.Record
|
||||
|
||||
# header
|
||||
h = header(reader)
|
||||
@test string.(findall(header(reader), "SQ")) == ["@SQ\tSN:CHROMOSOME_I\tLN:1009800"]
|
||||
|
||||
# first record
|
||||
record = SAM.Record()
|
||||
read!(reader, record)
|
||||
@test SAM.ismapped(record)
|
||||
@test SAM.refname(record) == "CHROMOSOME_I"
|
||||
@test SAM.position(record) == leftposition(record) == 2
|
||||
@test SAM.rightposition(record) == rightposition(record) == 102
|
||||
@test SAM.tempname(record) == seqname(record) == "SRR065390.14978392"
|
||||
@test SAM.sequence(record) == sequence(record) == dna"CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA"
|
||||
@test SAM.sequence(String, record) == "CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA"
|
||||
@test SAM.seqlength(record) == 100
|
||||
@test SAM.quality(record) == (b"#############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC" .- 33)
|
||||
@test SAM.quality(String, record) == "#############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC"
|
||||
@test SAM.flag(record) == 16
|
||||
@test SAM.cigar(record) == "27M1D73M"
|
||||
@test SAM.alignment(record) == Alignment([
|
||||
AlignmentAnchor( 0, 1, OP_START),
|
||||
AlignmentAnchor( 27, 28, OP_MATCH),
|
||||
AlignmentAnchor( 27, 29, OP_DELETE),
|
||||
AlignmentAnchor(100, 102, OP_MATCH)])
|
||||
@test record["XG"] == 1
|
||||
@test record["XM"] == 5
|
||||
@test record["XN"] == 0
|
||||
@test record["XO"] == 1
|
||||
@test record["AS"] == -18
|
||||
@test record["XS"] == -18
|
||||
@test record["YT"] == "UU"
|
||||
@test eof(reader)
|
||||
close(reader)
|
||||
|
||||
# rightposition (also implicitly alignlength)
|
||||
records = collect(open(SAM.Reader, joinpath(samdir, "ce#5b.sam")))
|
||||
@test SAM.rightposition(records[6]) == rightposition(records[6]) == 83
|
||||
|
||||
# iterator
|
||||
@test length(collect(open(SAM.Reader, joinpath(samdir, "ce#1.sam")))) == 1
|
||||
@test length(collect(open(SAM.Reader, joinpath(samdir, "ce#2.sam")))) == 2
|
||||
|
||||
# IOStream
|
||||
@test length(collect(SAM.Reader(open(joinpath(samdir, "ce#1.sam"))))) == 1
|
||||
@test length(collect(SAM.Reader(open(joinpath(samdir, "ce#2.sam"))))) == 2
|
||||
end
|
||||
|
||||
@testset "Round trip" begin
|
||||
function compare_records(xs, ys)
|
||||
if length(xs) != length(ys)
|
||||
return false
|
||||
end
|
||||
for (x, y) in zip(xs, ys)
|
||||
if x.data[x.filled] != y.data[y.filled]
|
||||
return false
|
||||
end
|
||||
end
|
||||
return true
|
||||
end
|
||||
for specimen in list_valid_specimens("SAM")
|
||||
filepath = joinpath(samdir, filename(specimen))
|
||||
mktemp() do path, io
|
||||
# copy
|
||||
reader = open(SAM.Reader, filepath)
|
||||
|
||||
header_original = header(reader)
|
||||
|
||||
writer = SAM.Writer(io, header_original)
|
||||
|
||||
records = SAM.Record[]
|
||||
for record in reader
|
||||
push!(records, record)
|
||||
write(writer, record)
|
||||
end
|
||||
|
||||
close(reader)
|
||||
close(writer)
|
||||
|
||||
reader = open(SAM.Reader, path)
|
||||
|
||||
@test header(reader) == header_original
|
||||
@test compare_records(collect(reader), records)
|
||||
|
||||
close(reader)
|
||||
|
||||
end
|
||||
end
|
||||
end
|
||||
|
||||
@testset "In-Place-Reading Pattern" begin
|
||||
|
||||
file_sam = joinpath(samdir, "ce#5b.sam")
|
||||
|
||||
records = open(collect, SAM.Reader, file_sam)
|
||||
|
||||
reader = open(SAM.Reader, file_sam)
|
||||
record = SAM.Record()
|
||||
i = 0
|
||||
while !eof(reader)
|
||||
empty!(record) # Reset the record.
|
||||
read!(reader, record)
|
||||
|
||||
i = i + 1
|
||||
|
||||
@test records[i] == record
|
||||
|
||||
end
|
||||
|
||||
close(reader)
|
||||
|
||||
end
|
||||
end
|
||||
Loading…
Reference in a new issue