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Cater for blank sam files
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parent
64f371e1e4
commit
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2 changed files with 17 additions and 7 deletions
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@ -94,17 +94,21 @@ end
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Read a `Record` into `rec`; overwriting or adding to existing field values.
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It is assumed that `rec` is already initialized or empty.
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"""
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function Base.read!(rdr::Reader, rec::Record)
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function Base.read!(rdr::Reader, record::Record)
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cs, ln, f = readrecord!(rdr.state.stream, rec, (rdr.state.state, rdr.state.linenum))
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cs, ln, found = readrecord!(rdr.state.stream, record, (rdr.state.state, rdr.state.linenum))
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rdr.state.state = cs
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rdr.state.linenum = ln
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rdr.state.filled = f
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rdr.state.filled = found
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if !f
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cs == 0 && throw(EOFError())
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throw(ArgumentError("malformed SAM file"))
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if found
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return record
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end
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return rec
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if cs == 0 || eof(rdr.state.stream)
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throw(EOFError())
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end
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throw(ArgumentError("malformed SAM file"))
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end
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@ -194,5 +194,11 @@
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close(reader)
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# Test blank file.
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file_sam = joinpath(samdir, "xx#blank.sam")
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records = open(collect, SAM.Reader, file_sam)
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@test records == []
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end
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end
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