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Use FormatSpecimens
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2 changed files with 11 additions and 11 deletions
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@ -26,8 +26,8 @@ Indexes = "0.1"
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julia = "1.1"
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[extras]
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FormatSpecimens = "3372ea36-2a1a-11e9-3eb7-996970b6ffbd"
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Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
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YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"
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[targets]
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test = ["Test", "YAML"]
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test = ["FormatSpecimens", "Test"]
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@ -2,11 +2,11 @@ using Test
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using GenomicFeatures
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using XAM
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import BioAlignments: Alignment, AlignmentAnchor, OP_START, OP_MATCH, OP_DELETE
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using FormatSpecimens
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import BGZFStreams: BGZFStream
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import BioCore.Exceptions: MissingFieldException
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import BioCore.Testing.get_bio_fmt_specimens
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import BioSequences: @dna_str, @aa_str
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import YAML
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import BioCore:
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header,
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@ -32,7 +32,7 @@ function randrange(range)
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end
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@testset "SAM" begin
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samdir = joinpath(get_bio_fmt_specimens("master", false, true), "SAM")
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samdir = path_of_format("SAM")
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@testset "MetaInfo" begin
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metainfo = SAM.MetaInfo()
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@ -172,8 +172,8 @@ end
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end
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return true
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end
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for specimen in YAML.load_file(joinpath(samdir, "index.yml"))
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filepath = joinpath(samdir, specimen["filename"])
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for specimen in list_valid_specimens("SAM")
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filepath = joinpath(samdir, filename(specimen))
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mktemp() do path, io
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# copy
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reader = open(SAM.Reader, filepath)
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@ -192,7 +192,7 @@ end
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end
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@testset "BAM" begin
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bamdir = joinpath(get_bio_fmt_specimens("master", false), "BAM")
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bamdir = path_of_format("BAM")
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@testset "AuxData" begin
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auxdata = BAM.AuxData(UInt8[])
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@ -370,11 +370,11 @@ end
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end
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@testset "Round trip" begin
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for specimen in YAML.load_file(joinpath(bamdir, "index.yml"))
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filepath = joinpath(bamdir, specimen["filename"])
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for specimen in list_valid_specimens("BAM")
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filepath = joinpath(bamdir, filename(specimen))
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mktemp() do path, _
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# copy
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if occursin("bai", get(specimen, "tags", ""))
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if hastags(specimen) && in("bai", tags(specimen))
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reader = open(BAM.Reader, filepath, index=filepath * ".bai")
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else
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reader = open(BAM.Reader, filepath)
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