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Do not allow unused trailing bytes in BAM records #71

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Do not allow unused trailing bytes in BAM records #71

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6 changes: 2 additions & 4 deletions src/bam/reader.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -130,10 +130,8 @@ function _read!(reader::Reader, record)
reader.stream,
pointer_from_objref(record),
FIXED_FIELDS_BYTES)
dsize = data_size(record)
if length(record.data) < dsize
resize!(record.data, dsize)
end
dsize = record.block_size - FIXED_FIELDS_BYTES + sizeof(record.block_size)
resize!(record.data, dsize)
unsafe_read(reader.stream, pointer(record.data), dsize)
record.reader = reader
return record
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27 changes: 10 additions & 17 deletions src/bam/record.jl
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Expand Up @@ -20,7 +20,7 @@ mutable struct Record <: XAMRecord
next_refid::Int32
next_pos::Int32
tlen::Int32
# variable length data
# This vector never has unused bytes at the end
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This comment may be confusing outside the context of the previous design, maybe

Suggested change
# This vector never has unused bytes at the end
# This vector used to have unused bytes at the end, but no longer does

or something?

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The original comment intended to distinguish the fields that could vary in length from those that do not. From that standpoint, it does not need changing. If you'd like to add a comment specific to a field, perhaps it should go on the same line as the field.

data::Vector{UInt8}
reader::Union{Reader, Nothing}

Expand All @@ -41,7 +41,7 @@ function Base.convert(::Type{Record}, data::Vector{UInt8})
record = Record()
dst_pointer = Ptr{UInt8}(pointer_from_objref(record))
unsafe_copyto!(dst_pointer, pointer(data), FIXED_FIELDS_BYTES)
dsize = data_size(record)
dsize = record.block_size - FIXED_FIELDS_BYTES + sizeof(record.block_size)
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This calculation occurs more than once. It deserves its own function, which may be separate from data_size.

resize!(record.data, dsize)
length(data) < dsize + FIXED_FIELDS_BYTES && throw(ArgumentError("data too short"))
unsafe_copyto!(record.data, 1, data, FIXED_FIELDS_BYTES + 1, dsize)
Expand All @@ -61,19 +61,19 @@ function Base.:(==)(a::Record, b::Record)
a.next_refid == b.next_refid &&
a.next_pos == b.next_pos &&
a.tlen == b.tlen &&
a.data[1:data_size(a)] == b.data[1:data_size(b)]
a.data == b.data
end

function Base.copy(record::Record)
copy = Record()
GC.@preserve copy record begin
dst_pointer = Ptr{UInt8}(pointer_from_objref(copy))
cp = Record()
GC.@preserve cp record begin
dst_pointer = Ptr{UInt8}(pointer_from_objref(cp))
src_pointer = Ptr{UInt8}(pointer_from_objref(record))
unsafe_copyto!(dst_pointer, src_pointer, FIXED_FIELDS_BYTES)
end
copy.data = record.data[1:data_size(record)]
copy.reader = record.reader
return copy
cp.data = copy(record.data)
cp.reader = record.reader
return cp
end

function Base.empty!(record::Record)
Expand Down Expand Up @@ -584,14 +584,7 @@ end
# ----------------

# Return the size of the `.data` field.
function data_size(record::Record)
if isfilled(record)
return record.block_size - FIXED_FIELDS_BYTES + sizeof(record.block_size)
end

return 0

end
data_size(record::Record) = isfilled(record) ? length(record.data) : 0

function checkfilled(record::Record)
if !isfilled(record)
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