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Minimal adjustements
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parent
433b8d14e8
commit
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2 changed files with 18 additions and 13 deletions
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@ -511,9 +511,12 @@ end
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Get the segment sequence of `record`.
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Get the segment sequence of `record`.
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"""
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"""
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function sequence(record::Record)::BioSequences.LongDNASeq
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function sequence(record::Record)
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checkfilled(record)
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checkfilled(record)
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seqlen = seqlength(record)
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seqlen = seqlength(record)
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if seqlen == 0
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return nothing
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end
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data = Vector{UInt64}(undef, cld(seqlen, 16))
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data = Vector{UInt64}(undef, cld(seqlen, 16))
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src::Ptr{UInt64} = pointer(record.data, seqname_length(record) + n_cigar_op(record, false) * 4 + 1)
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src::Ptr{UInt64} = pointer(record.data, seqname_length(record) + n_cigar_op(record, false) * 4 + 1)
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for i in 1:lastindex(data)
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for i in 1:lastindex(data)
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@ -206,9 +206,9 @@ Get the 1-based leftmost mapping position of `record`.
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function position(record::Record)::Int
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function position(record::Record)::Int
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checkfilled(record)
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checkfilled(record)
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pos = unsafe_parse_decimal(Int, record.data, record.pos)
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pos = unsafe_parse_decimal(Int, record.data, record.pos)
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if pos == 0
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# if pos == 0
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missingerror(:position)
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# missingerror(:position)
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end
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# end
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return pos
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return pos
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end
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end
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@ -263,9 +263,9 @@ Get the position of the mate/next read of `record`.
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function nextposition(record::Record)::Int
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function nextposition(record::Record)::Int
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checkfilled(record)
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checkfilled(record)
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pos = unsafe_parse_decimal(Int, record.data, record.pnext)
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pos = unsafe_parse_decimal(Int, record.data, record.pnext)
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if pos == 0
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# if pos == 0
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missingerror(:nextposition)
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# missingerror(:nextposition)
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end
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# end
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return pos
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return pos
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end
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end
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@ -299,7 +299,8 @@ Get the CIGAR string of `record`.
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function cigar(record::Record)::String
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function cigar(record::Record)::String
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checkfilled(record)
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checkfilled(record)
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if ismissing(record, record.cigar)
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if ismissing(record, record.cigar)
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missingerror(:cigar)
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# missingerror(:cigar)
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return ""
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end
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end
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return String(record.data[record.cigar])
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return String(record.data[record.cigar])
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end
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end
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@ -377,9 +378,9 @@ Get the template length of `record`.
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function templength(record::Record)::Int
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function templength(record::Record)::Int
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checkfilled(record)
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checkfilled(record)
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len = unsafe_parse_decimal(Int, record.data, record.tlen)
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len = unsafe_parse_decimal(Int, record.data, record.tlen)
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if len == 0
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# if len == 0
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missingerror(:tlen)
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# missingerror(:tlen)
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end
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# end
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return len
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return len
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end
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end
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@ -392,10 +393,11 @@ end
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Get the segment sequence of `record`.
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Get the segment sequence of `record`.
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"""
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"""
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function sequence(record::Record)::BioSequences.LongDNASeq
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function sequence(record::Record)
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checkfilled(record)
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checkfilled(record)
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if ismissing(record, record.seq)
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if ismissing(record, record.seq)
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missingerror(:sequence)
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# missingerror(:sequence)
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return nothing
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end
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end
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seqlen = length(record.seq)
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seqlen = length(record.seq)
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ret = BioSequences.LongDNASeq(seqlen)
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ret = BioSequences.LongDNASeq(seqlen)
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