mirror of
https://github.com/MillironX/XAM.jl.git
synced 2024-11-23 02:09:55 +00:00
Improve documentation of flag function
This commit is contained in:
parent
18dae0d45d
commit
a72fcf47cb
6 changed files with 29 additions and 12 deletions
21
src/XAM.jl
21
src/XAM.jl
|
@ -4,6 +4,27 @@ export
|
|||
SAM,
|
||||
BAM
|
||||
|
||||
"""
|
||||
flag(record::Union{SAM.Record, BAM.Record})::UInt16
|
||||
|
||||
Get the bitwise flags of `record`. The returned value is a `UInt16` of each flag
|
||||
being OR'd together. The possible flags are:
|
||||
|
||||
0x0001 template having multiple segments in sequencing
|
||||
0x0002 each segment properly aligned according to the aligner
|
||||
0x0004 segment unmapped
|
||||
0x0008 next segment in the template unmapped
|
||||
0x0010 SEQ being reverse complemented
|
||||
0x0020 SEQ of the next segment in the template being reverse complemented
|
||||
0x0040 the first segment in the template
|
||||
0x0080 the last segment in the template
|
||||
0x0100 secondary alignment
|
||||
0x0200 not passing filters, such as platform/vendor quality controls
|
||||
0x0400 PCR or optical duplicate
|
||||
0x0800 supplementary alignment
|
||||
"""
|
||||
function flag end
|
||||
|
||||
include("sam/sam.jl")
|
||||
include("bam/bam.jl")
|
||||
|
||||
|
|
|
@ -6,6 +6,7 @@ module BAM
|
|||
using BioGenerics
|
||||
using GenomicFeatures
|
||||
using XAM.SAM
|
||||
import ..XAM: flag
|
||||
|
||||
import BGZFStreams
|
||||
import BioAlignments
|
||||
|
|
|
@ -128,11 +128,6 @@ end
|
|||
# Accessor Fuctions
|
||||
# -----------------
|
||||
|
||||
"""
|
||||
flag(record::Record)::UInt16
|
||||
|
||||
Get the bitwise flag of `record`.
|
||||
"""
|
||||
function flag(record::Record)::UInt16
|
||||
checkfilled(record)
|
||||
return record.flag
|
||||
|
|
|
@ -18,9 +18,13 @@ for (name, bits, doc) in [
|
|||
(:SUPPLEMENTARY, UInt16(0x800), "supplementary alignment" ),]
|
||||
@assert bits isa UInt16
|
||||
sym = Symbol("FLAG_", name)
|
||||
doc = string(@sprintf("0x%04x: ", bits), doc)
|
||||
docstring = """ $sym
|
||||
SAM/BAM flag: $doc
|
||||
|
||||
See also: [`flag`](@ref)
|
||||
"""
|
||||
@eval begin
|
||||
@doc $(doc) const $(sym) = $(bits)
|
||||
@doc $(docstring) const $(sym) = $(bits)
|
||||
end
|
||||
end
|
||||
|
||||
|
|
|
@ -150,11 +150,6 @@ end
|
|||
# Accessor Functions
|
||||
# ------------------
|
||||
|
||||
"""
|
||||
flag(record::Record)::UInt16
|
||||
|
||||
Get the bitwise flag of `record`.
|
||||
"""
|
||||
function flag(record::Record)::UInt16
|
||||
checkfilled(record)
|
||||
return unsafe_parse_decimal(UInt16, record.data, record.flag)
|
||||
|
|
|
@ -11,6 +11,7 @@ import BioGenerics.Exceptions: missingerror
|
|||
import BioGenerics.Automa: State
|
||||
import BioSequences
|
||||
import TranscodingStreams: TranscodingStreams, TranscodingStream
|
||||
import ..XAM: flag
|
||||
|
||||
using Printf: @sprintf
|
||||
|
||||
|
|
Loading…
Reference in a new issue