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https://github.com/MillironX/XAM.jl.git
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Make BAM record layout match BAM specs
This commit is contained in:
Jakob Nissen
Ciarán O'Mara
parent
8836b4dbb6
commit
b086fefbd5
2 changed files with 46 additions and 37 deletions
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@ -11,18 +11,21 @@ mutable struct Record
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block_size::Int32
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refid::Int32
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pos::Int32
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bin_mq_nl::UInt32
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flag_nc::UInt32
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l_read_name::UInt8
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mapq::UInt8
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bin::UInt16
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n_cigar_op::UInt16
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flag::UInt16
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l_seq::Int32
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next_refid::Int32
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next_pos::Int32
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tlen::Int32
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# variable length data
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data::Vector{UInt8}
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reader::Reader
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reader::Union{Reader, Nothing}
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function Record()
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return new(0, 0, 0, 0, 0, 0, 0, 0, 0, UInt8[])
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return new(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, UInt8[])
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end
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end
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@ -49,8 +52,11 @@ function Base.:(==)(a::Record, b::Record)
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return a.block_size == b.block_size &&
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a.refid == b.refid &&
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a.pos == b.pos &&
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a.bin_mq_nl == b.bin_mq_nl &&
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a.flag_nc == b.flag_nc &&
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a.l_read_name == b.l_read_name &&
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a.mapq == b.mapq &&
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a.bin == b.bin &&
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a.n_cigar_op == b.n_cigar_op &&
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a.flag == b.flag &&
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a.l_seq == b.l_seq &&
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a.next_refid == b.next_refid &&
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a.next_pos == b.next_pos &&
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@ -60,19 +66,13 @@ end
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function Base.copy(record::Record)
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copy = Record()
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copy.block_size = record.block_size
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copy.refid = record.refid
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copy.pos = record.pos
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copy.bin_mq_nl = record.bin_mq_nl
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copy.flag_nc = record.flag_nc
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copy.l_seq = record.l_seq
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copy.next_refid = record.next_refid
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copy.next_pos = record.next_pos
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copy.tlen = record.tlen
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copy.data = record.data[1:data_size(record)]
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if isdefined(record, :reader)
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copy.reader = record.reader
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GC.@preserve copy record begin
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dst_pointer = Ptr{UInt8}(pointer_from_objref(copy))
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src_pointer = Ptr{UInt8}(pointer_from_objref(record))
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unsafe_copyto!(dst_pointer, src_pointer, FIXED_FIELDS_BYTES)
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end
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copy.data = record.data[1:data_size(record)]
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copy.reader = record.reader
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return copy
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end
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@ -80,8 +80,11 @@ function Base.empty!(record::Record)
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record.block_size = 0
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record.refid = 0
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record.pos = 0
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record.bin_mq_nl = 0
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record.flag_nc = 0
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record.l_read_name = 0
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record.mapq = 0
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record.bin = 0
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record.flag = 0
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record.n_cigar_op = 0
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record.l_seq = 0
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record.next_refid = 0
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record.next_pos = 0
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@ -132,7 +135,7 @@ Get the bitwise flag of `record`.
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"""
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function flag(record::Record)::UInt16
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checkfilled(record)
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return UInt16(record.flag_nc >> 16)
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return record.flag
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end
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function hasflag(record::Record)
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@ -318,7 +321,7 @@ end
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Get the mapping quality of `record`.
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"""
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function mappingquality(record::Record)::UInt8
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return UInt8((record.bin_mq_nl >> 8) & 0xff)
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return record.mapq
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end
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function hasmappingquality(record::Record)
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@ -397,7 +400,7 @@ function extract_cigar_rle(data::Vector{UInt8}, offset, n)
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end
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function cigar_position(record::Record, checkCG::Bool = true)::Tuple{Int, Int}
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cigaridx, nops = seqname_length(record) + 1, record.flag_nc & 0xFFFF
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cigaridx, nops = seqname_length(record) + 1, record.n_cigar_op
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if !checkCG
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return cigaridx, nops
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end
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@ -664,5 +667,5 @@ end
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# Return the length of the read name.
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function seqname_length(record::Record)
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return record.bin_mq_nl & 0xff
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return record.l_read_name
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end
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@ -104,9 +104,12 @@
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unsafe_copyto!(array, BAM.FIXED_FIELDS_BYTES + 1, record.data, 1, dsize)
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end
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new_record = convert(BAM.Record, array)
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@test record.bin_mq_nl == new_record.bin_mq_nl
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@test record.l_read_name == new_record.l_read_name
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@test record.mapq == new_record.mapq
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@test record.bin == new_record.bin
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@test record.block_size == new_record.block_size
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@test record.flag_nc == new_record.flag_nc
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@test record.flag == new_record.flag
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@test record.n_cigar_op == new_record.n_cigar_op
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@test record.l_seq == new_record.l_seq
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@test record.next_refid == new_record.next_refid
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@test record.next_pos == new_record.next_pos
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@ -162,18 +165,21 @@
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if length(xs) != length(ys)
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return false
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end
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for (x, y) in zip(xs, ys)
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for (a, b) in zip(xs, ys)
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if !(
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x.block_size == y.block_size &&
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x.refid == y.refid &&
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x.pos == y.pos &&
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x.bin_mq_nl == y.bin_mq_nl &&
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x.flag_nc == y.flag_nc &&
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x.l_seq == y.l_seq &&
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x.next_refid == y.next_refid &&
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x.next_pos == y.next_pos &&
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x.tlen == y.tlen &&
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x.data[1:BAM.data_size(x)] == y.data[1:BAM.data_size(y)])
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a.block_size == b.block_size &&
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a.refid == b.refid &&
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a.pos == b.pos &&
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a.l_read_name == b.l_read_name &&
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a.mapq == b.mapq &&
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a.bin == b.bin &&
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a.n_cigar_op == b.n_cigar_op &&
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a.flag == b.flag &&
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a.l_seq == b.l_seq &&
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a.next_refid == b.next_refid &&
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a.next_pos == b.next_pos &&
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a.tlen == b.tlen &&
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a.data[1:BAM.data_size(a)] == b.data[1:BAM.data_size(b)])
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return false
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end
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end
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