millironx/XAM.jl
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This commit is contained in:
Ciarán O’Mara 2021-06-27 20:41:58 +10:00
parent 8f26bbf4a7
commit ccc91123d6
2 changed files with 7 additions and 4 deletions
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2
src/sam/reader.jl
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@ -12,7 +12,7 @@ function Reader(state::State{S}) where {S <: TranscodingStream}
cs, ln = readheader!(rdr.state.stream, rdr.header, (sam_machine_header.start_state, rdr.state.linenum)) cs, ln = readheader!(rdr.state.stream, rdr.header, (sam_machine_header.start_state, rdr.state.linenum))
rdr.state.state = sam_machine_body.start_state rdr.state.state = sam_machine_body.start_state # Get the reader ready to read the body.
rdr.state.linenum = ln rdr.state.linenum = ln
rdr.state.filled = false rdr.state.filled = false

9
src/sam/record.jl
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@ -2,10 +2,11 @@
# ========== # ==========
mutable struct Record mutable struct Record
# data and filled range # Data and filled range.
data::Vector{UInt8} data::Vector{UInt8}
filled::UnitRange{Int} filled::UnitRange{Int} # Note: Specifies the data in use.
# indexes
# Mandatory fields.
qname::UnitRange{Int} qname::UnitRange{Int}
flag::UnitRange{Int} flag::UnitRange{Int}
rname::UnitRange{Int} rname::UnitRange{Int}
@ -17,6 +18,8 @@ mutable struct Record
tlen::UnitRange{Int} tlen::UnitRange{Int}
seq::UnitRange{Int} seq::UnitRange{Int}
qual::UnitRange{Int} qual::UnitRange{Int}
# Auxiliary fields.
fields::Vector{UnitRange{Int}} fields::Vector{UnitRange{Int}}
end end