Pluralise flag

CHANGELOG.md

@@ -22,6 +22,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Improved Slack link.
 - Updated to use [Automa](https://github.com/BioJulia/Automa.jl) v1 ([#65](https://github.com/BioJulia/XAM.jl/pull/65)).
 - Pointed the Unit Tests badge at the develop branch.
+- Pluralised flag.
 
 ### Fixed
 - Updated hts-files.md ([#62](https://github.com/BioJulia/XAM.jl/pull/62)).

docs/src/man/hts-files.md

@@ -110,7 +110,7 @@ In the above we can see there were 7 sequences in the reference: 5 chromosomes,
 The `XAM` package supports the following accessors for `SAM.Record` types.
 
 ```@docs
-XAM.SAM.flag
+XAM.SAM.flags
 XAM.SAM.ismapped
 XAM.SAM.isprimary
 XAM.SAM.refname
@@ -135,7 +135,7 @@ XAM.SAM.auxdata
 The `XAM` package supports the following accessors for `BAM.Record` types.
 
 ```@docs
-XAM.BAM.flag
+XAM.BAM.flags
 XAM.BAM.ismapped
 XAM.BAM.isprimary
 XAM.BAM.refid

src/bam/bam.jl

@@ -6,7 +6,7 @@ module BAM
 using BioGenerics
 using GenomicFeatures
 using XAM.SAM
-import ..XAM: flag, XAMRecord, XAMReader, XAMWriter,
+import ..XAM: flags, XAMRecord, XAMReader, XAMWriter,
 	ismapped, isprimary, ispositivestrand, isnextmapped #TODO: Deprecate import of flag queries. These were imported to preseve existing API.
 
 import BGZFStreams

src/bam/record.jl

@@ -15,7 +15,7 @@ mutable struct Record <: XAMRecord
     mapq::UInt8
     bin::UInt16
     n_cigar_op::UInt16
-    flag::UInt16
+    flags::UInt16
     l_seq::Int32
     next_refid::Int32
     next_pos::Int32
@@ -56,7 +56,7 @@ function Base.:(==)(a::Record, b::Record)
         a.mapq          == b.mapq &&
         a.bin           == b.bin &&
         a.n_cigar_op    == b.n_cigar_op &&
-        a.flag          == b.flag &&
+        a.flags         == b.flags &&
         a.l_seq         == b.l_seq &&
         a.next_refid    == b.next_refid &&
         a.next_pos      == b.next_pos &&
@@ -83,7 +83,7 @@ function Base.empty!(record::Record)
     record.l_read_name = 0
     record.mapq = 0
     record.bin = 0
-    record.flag = 0
+    record.flags = 0
     record.n_cigar_op = 0
     record.l_seq      = 0
     record.next_refid = 0
@@ -100,7 +100,7 @@ function Base.show(io::IO, record::Record)
     if isfilled(record)
         println(io)
         println(io, "      template name: ", tempname(record))
-        println(io, "               flag: ", flag(record))
+        println(io, "              flags: ", flags(record))
         println(io, "       reference ID: ", refid(record))
         println(io, "           position: ", position(record))
         println(io, "    mapping quality: ", mappingquality(record))
@@ -128,12 +128,12 @@ end
 # Accessor Fuctions
 # -----------------
 
-function flag(record::Record)::UInt16
+function flags(record::Record)::UInt16
     checkfilled(record)
-    return record.flag
+    return record.flags
 end
 
-function hasflag(record::Record)
+function hasflags(record::Record)
     return isfilled(record)
 end
 

src/flags.jl

@@ -3,7 +3,7 @@
 #
 
 """
-    flag(record::XAMRecord})::UInt16
+    flags(record::XAMRecord})::UInt16
 
 Get the bitwise flags of `record`.
 The returned value is a `UInt16` of each flag being OR'd together.
@@ -23,9 +23,9 @@ The possible flags are:
     0x0800 supplementary alignment
 """
 
-function flag end
+function flags end
 
-# Bitwise flags (or FLAG).
+# Bitwise flag (or FLAG).
 for (name, bits, doc) in [
         (:PAIRED,        UInt16(0x001), "the read is paired in sequencing, no matter whether it is mapped in a pair"),
         (:PROPER_PAIR,   UInt16(0x002), "the read is mapped in a proper pair"                                       ),
@@ -44,7 +44,7 @@ for (name, bits, doc) in [
     docstring = """    $sym
     SAM/BAM flag: $doc
 
-    See also: [`flag`](@ref)
+    See also: [`flags`](@ref)
     """
     @eval begin
         @doc $(docstring) const $(sym) = $(bits)
@@ -57,7 +57,7 @@ end
 Query whether the `record`'s template has multiple segments in sequencing.
 """
 function ispaired(record::XAMRecord)::Bool
-    return flag(record) & FLAG_PAIRED == FLAG_PAIRED
+    return flags(record) & FLAG_PAIRED == FLAG_PAIRED
 end
 
 """
@@ -66,7 +66,7 @@ end
 Query whether each segment of the `record`'s template properly aligned according to the aligner.
 """
 function isproperpair(record::XAMRecord)::Bool
-    return flag(record) & PROPER_PAIR == PROPER_PAIR
+    return flags(record) & PROPER_PAIR == PROPER_PAIR
 end
 
 """
@@ -75,7 +75,7 @@ end
 Query whether the `record` is unmapped.
 """
 function isunmapped(record::XAMRecord)::Bool
-    return flag(record) & FLAG_UNMAP == FLAG_UNMAP
+    return flags(record) & FLAG_UNMAP == FLAG_UNMAP
 end
 
 """
@@ -84,8 +84,8 @@ end
 Query whether the `record` is mapped.
 """
 function ismapped(record::XAMRecord)::Bool
-    # return flag(record) & FLAG_UNMAP == 0
-    return isfilled(record) && (flag(record) & FLAG_UNMAP == 0)
+    # return flags(record) & FLAG_UNMAP == 0
+    return isfilled(record) && (flags(record) & FLAG_UNMAP == 0)
 end
 
 """
@@ -94,7 +94,7 @@ end
 Query whether the `record`'s mate is unmapped.
 """
 function ismateunmapped(record::XAMRecord)::Bool
-    return flag(record) & FLAG_MUNMAP == FLAG_MUNMAP
+    return flags(record) & FLAG_MUNMAP == FLAG_MUNMAP
 end
 
 """
@@ -103,7 +103,7 @@ end
 Test if the mate/next read of `record` is mapped.
 """
 function isnextmapped(record::XAMRecord)::Bool
-    return flag(record) & FLAG_MUNMAP == 0
+    return flags(record) & FLAG_MUNMAP == 0
 end
 
 """
@@ -112,7 +112,7 @@ end
 Query whether the `record` is mapped to the reverse strand.
 """
 function isreverse(record::XAMRecord)::Bool
-    return flag(record) & FLAG_REVERSE == FLAG_REVERSE
+    return flags(record) & FLAG_REVERSE == FLAG_REVERSE
 end
 
 """
@@ -121,7 +121,7 @@ end
 Query whether the `record` is mapped to the forward strand.
 """
 function isforward(record::XAMRecord)::Bool
-    return flag(record) & FLAG_REVERSE == 0
+    return flags(record) & FLAG_REVERSE == 0
 end
 
 """
@@ -148,7 +148,7 @@ end
 Query whether the `record`'s mate is mapped to the reverse strand.
 """
 function ismatereverse(record::XAMRecord)::Bool
-    return flag(record) & FLAG_MREVERSE == FLAG_MREVERSE
+    return flags(record) & FLAG_MREVERSE == FLAG_MREVERSE
 end
 
 """
@@ -157,7 +157,7 @@ end
 Query whether the `record` is read1.
 """
 function isread1(record::XAMRecord)::Bool
-    return flag(record) & FLAG_READ1 == FLAG_READ1
+    return flags(record) & FLAG_READ1 == FLAG_READ1
 end
 
 """
@@ -166,7 +166,7 @@ end
 Query whether the `record` is read2.
 """
 function isread2(record::XAMRecord)::Bool
-    return flag(record) & FLAG_READ2 == FLAG_READ2
+    return flags(record) & FLAG_READ2 == FLAG_READ2
 end
 
 """
@@ -175,7 +175,7 @@ end
 Query whether the `record` is a secondary alignment.
 """
 function issecondaryalignment(record::XAMRecord)::Bool
-    return flag(record) & FLAG_SECONDARY == FLAG_SECONDARY
+    return flags(record) & FLAG_SECONDARY == FLAG_SECONDARY
 end
 
 """
@@ -184,7 +184,7 @@ end
 Query whether the `record` is the primary alignment.
 """
 function isprimaryalignment(record::XAMRecord)::Bool
-    return flag(record) & FLAG_SECONDARY == 0
+    return flags(record) & FLAG_SECONDARY == 0
 end
 
 """
@@ -193,7 +193,7 @@ end
 Query whether the `record` did not pass filters, such as platform/vendor quality controls.
 """
 function isqcfail(record::XAMRecord)::Bool
-    return flag(record) & FLAG_QCFAIL == FLAG_QCFAIL
+    return flags(record) & FLAG_QCFAIL == FLAG_QCFAIL
 end
 
 """
@@ -202,7 +202,7 @@ end
 Query whether the `record` is a PCR or optical duplicate.
 """
 function isduplicate(record::XAMRecord)::Bool
-    return flag(record) & FLAG_DUP == FLAG_DUP
+    return flags(record) & FLAG_DUP == FLAG_DUP
 end
 
 """
@@ -211,16 +211,16 @@ end
 Query whether the `record` is a supplementary alignment.
 """
 function issupplementaryalignment(record::XAMRecord)::Bool
-    return flag(record) & FLAG_SUPPLEMENTARY == FLAG_SUPPLEMENTARY
+    return flags(record) & FLAG_SUPPLEMENTARY == FLAG_SUPPLEMENTARY
 end
 
 """
     isprimary(record::XAMRecord)::Bool
 
 Query whether `record` is a primary line of the read.
 
-This is equivalent to `flag(record) & 0x900 == 0`.
+This is equivalent to `flags(record) & 0x900 == 0`.
 """
 function isprimary(record::XAMRecord)::Bool
-    return flag(record) & 0x900 == 0
+    return flags(record) & 0x900 == 0
 end

src/sam/readrecord.jl

@@ -28,7 +28,7 @@ const sam_machine_metainfo, sam_machine_record, sam_machine_header, sam_machine_
 
     record = let
         qname = onexit!(onenter!(re"[!-?A-~]+", :pos), :record_qname)
-        flag = onexit!(onenter!(re"[0-9]+", :pos), :record_flag)
+        flags = onexit!(onenter!(re"[0-9]+", :pos), :record_flags)
         rname = onexit!(onenter!(re"\*|[!-()+-<>-~][!-~]*", :pos), :record_rname)
         pos = onexit!(onenter!(re"[0-9]+", :pos), :record_pos)
         mapq = onexit!(onenter!(re"[0-9]+", :pos), :record_mapq)
@@ -54,7 +54,7 @@ const sam_machine_metainfo, sam_machine_record, sam_machine_header, sam_machine_
         onexit!(onenter!(field, :pos), :record_field)
 
         qname * '\t' *
-        flag  * '\t' *
+        flags * '\t' *
         rname * '\t' *
         pos   * '\t' *
         mapq  * '\t' *
@@ -129,7 +129,7 @@ const sam_actions_record = Dict(
     :mark => :(@mark),
     :pos => :(pos = @relpos(p)),
     :record_qname => :(record.qname = pos:@relpos(p-1)),
-    :record_flag  => :(record.flag  = pos:@relpos(p-1)),
+    :record_flags  => :(record.flags  = pos:@relpos(p-1)),
     :record_rname => :(record.rname = pos:@relpos(p-1)),
     :record_pos   => :(record.pos   = pos:@relpos(p-1)),
     :record_mapq  => :(record.mapq  = pos:@relpos(p-1)),

src/sam/record.jl

@@ -8,7 +8,7 @@ mutable struct Record <: XAMRecord
 
     # Mandatory fields.
     qname::UnitRange{Int}
-    flag::UnitRange{Int}
+    flags::UnitRange{Int}
     rname::UnitRange{Int}
     pos::UnitRange{Int}
     mapq::UnitRange{Int}
@@ -80,7 +80,7 @@ end
 function Base.:(==)(a::Record, b::Record)
     return a.filled == b.filled &&
         a.qname     == b.qname &&
-        a.flag      == b.flag &&
+        a.flags     == b.flags &&
         a.rname     == b.rname &&
         a.pos       == b.pos &&
         a.mapq      == b.mapq &&
@@ -99,7 +99,7 @@ function Base.show(io::IO, record::Record)
     if isfilled(record)
         println(io)
         println(io, "    template name: ", hastempname(record) ? tempname(record) : "<missing>")
-        println(io, "             flag: ", hasflag(record) ? flag(record) : "<missing>")
+        println(io, "            flags: ", hasflags(record) ? flags(record) : "<missing>")
         println(io, "        reference: ", hasrefname(record) ? refname(record) : "<missing>")
         println(io, "         position: ", hasposition(record) ? position(record) : "<missing>")
         println(io, "  mapping quality: ", hasmappingquality(record) ? mappingquality(record) : "<missing>")
@@ -133,7 +133,7 @@ function Base.copy(record::Record)
         copy(record.data),
         record.filled,
         record.qname,
-        record.flag,
+        record.flags,
         record.rname,
         record.pos,
         record.mapq,
@@ -150,12 +150,12 @@ end
 # Accessor Functions
 # ------------------
 
-function flag(record::Record)::UInt16
+function flags(record::Record)::UInt16
     checkfilled(record)
-    return unsafe_parse_decimal(UInt16, record.data, record.flag)
+    return unsafe_parse_decimal(UInt16, record.data, record.flags)
 end
 
-function hasflag(record::Record)
+function hasflags(record::Record)
     return isfilled(record)
 end
 
@@ -545,7 +545,7 @@ end
 function Base.empty!(record::Record)
     record.filled = 1:0
     record.qname = 1:0
-    record.flag = 1:0
+    record.flags = 1:0
     record.rname = 1:0
     record.pos = 1:0
     record.mapq = 1:0

src/sam/sam.jl

@@ -11,7 +11,7 @@ import BioGenerics.Exceptions: missingerror
 import BioGenerics.Automa: State
 import BioSequences
 import TranscodingStreams: TranscodingStreams, TranscodingStream
-import ..XAM: flag, XAMRecord, XAMReader, XAMWriter,
+import ..XAM: flags, XAMRecord, XAMReader, XAMWriter,
     ismapped, isprimary, ispositivestrand, isnextmapped #TODO: Deprecate import of flag queries. These were imported to preseve existing API.
 
 using Printf: @sprintf