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Check header in roundtrip

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This commit is contained in:
Ciarán O'Mara 2020-03-21 17:16:14 +11:00
parent 031751f6b3
commit f6846edfb1
1 changed files with 27 additions and 5 deletions
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32
test/runtests.jl
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@ -172,15 +172,27 @@ end
mktemp() do path, io
# copy
reader = open(SAM.Reader, filepath)
writer = SAM.Writer(io, header(reader))
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)
@test compare_records(open(collect, SAM.Reader, path), records)
reader = open(SAM.Reader, path)
@test header(reader) == header_original
@test compare_records(collect(reader), records)
close(reader)
end
end
end
@ -378,8 +390,11 @@ end
else
reader = open(BAM.Reader, filepath)
end
writer = BAM.Writer(
BGZFStream(path, "w"), BAM.header(reader, fillSQ=isempty(findall(header(reader), "SQ"))))
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)
@ -387,7 +402,14 @@ end
end
close(reader)
close(writer)
@test compare_records(open(collect, BAM.Reader, path), records)
reader = open(BAM.Reader, path)
@test header(reader) == header_original
@test compare_records(collect(reader), records)
close(reader)
end
end
end