Merge branch 'master' into develop

Project.toml

@@ -1,7 +1,7 @@
 name = "XAM"
 uuid = "d759349c-bcba-11e9-07c2-5b90f8f05f7c"
 authors = ["Kenta Sato <bicycle1885@gmail.com>", "Ben J. Ward <ward9250@gmail.com>", "Ciarán O'Mara <Ciaran.OMara@utas.edu.au>"]
-version = "0.2.2"
+version = "0.2.3"
 
 [deps]
 Automa = "67c07d97-cdcb-5c2c-af73-a7f9c32a568b"

docs/src/man/hts-files.md

@@ -58,6 +58,7 @@ In-place reading reuses a pre-allocated object for every record and less memory
 reader = open(BAM.Reader, "data.bam")
 record = BAM.Record()
 while !eof(reader)
+    empty!(record)
     read!(reader, record)
     # do something
 end

src/bam/reader.jl

@@ -72,12 +72,11 @@ function Base.seekstart(reader::Reader)
     seek(reader.stream, reader.start_offset)
 end
 
-function Base.iterate(reader::Reader, rec=Record())
+function Base.iterate(reader::Reader, nextone = Record())
-    if eof(reader)
+    if BioGenerics.IO.tryread!(reader, nextone) === nothing
         return nothing
     end
-    read!(reader, rec)
+    return copy(nextone), empty!(nextone)
-    return copy(rec), rec
 end
 
 # Initialize a BAM reader by reading the header section.

src/bam/record.jl

@@ -45,6 +45,19 @@ function Base.convert(::Type{Record}, data::Vector{UInt8})
     return record
 end
 
+function Base.:(==)(a::Record, b::Record)
+    return a.block_size == b.block_size &&
+        a.refid         == b.refid &&
+        a.pos           == b.pos &&
+        a.bin_mq_nl     == b.bin_mq_nl &&
+        a.flag_nc       == b.flag_nc &&
+        a.l_seq         == b.l_seq &&
+        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)]
+end
+
 function Base.copy(record::Record)
     copy = Record()
     copy.block_size = record.block_size
@@ -63,6 +76,22 @@ function Base.copy(record::Record)
     return copy
 end
 
+function Base.empty!(record::Record)
+    record.block_size = 0
+    record.refid      = 0
+    record.pos        = 0
+    record.bin_mq_nl  = 0
+    record.flag_nc    = 0
+    record.l_seq      = 0
+    record.next_refid = 0
+    record.next_pos   = 0
+    record.tlen       = 0
+
+    #Note: data will be overwritten and indexed using data_size.
+    
+    return record
+end
+
 function Base.show(io::IO, record::Record)
     print(io, summary(record), ':')
     if isfilled(record)

src/sam/reader.jl

@@ -81,9 +81,20 @@ function index!(record::Record)
     return record
 end
 
-function Base.read!(rdr::Reader, rec::Record)
+function Base.iterate(reader::Reader, nextone::Record = Record())
+    if BioGenerics.IO.tryread!(reader, nextone) === nothing
+        return nothing
+    end
+    return copy(nextone), empty!(nextone)
+end
 
-    empty!(rec.fields) #Note: data is pushed to the fields field, and other field data is overwritten. #TODO: distinguish for inplace reading pattern.
+"""
+    read!(rdr::Reader, rec::Record)
+
+Read a `Record` into `rec`; overwriting or adding to existing field values.
+It is assumed that `rec` is already initialized or empty.
+"""
+function Base.read!(rdr::Reader, rec::Record)
 
     cs, ln, f = readrecord!(rdr.state.stream, rec, (rdr.state.state, rdr.state.linenum))
 

src/sam/record.jl

@@ -74,6 +74,23 @@ function Base.convert(::Type{Record}, str::AbstractString)
     return Record(collect(UInt8, str))
 end
 
+function Base.:(==)(a::Record, b::Record)
+    return a.filled == b.filled &&
+        a.qname     == b.qname &&
+        a.flag      == b.flag &&
+        a.rname     == b.rname &&
+        a.pos       == b.pos &&
+        a.mapq      == b.mapq &&
+        a.cigar     == b.cigar &&
+        a.rnext     == b.rnext &&
+        a.pnext     == b.pnext &&
+        a.tlen      == b.tlen &&
+        a.seq       == b.seq &&
+        a.qual      == b.qual &&
+        a.fields    == b.fields &&
+        a.data[a.filled] == b.data[b.filled]
+end
+
 function Base.show(io::IO, record::Record)
     print(io, summary(record), ':')
     if isfilled(record)
@@ -554,7 +571,7 @@ end
 # Helper Functions
 # ----------------
 
-function initialize!(record::Record)
+function Base.empty!(record::Record)
     record.filled = 1:0
     record.qname = 1:0
     record.flag = 1:0
@@ -571,6 +588,10 @@ function initialize!(record::Record)
     return record
 end
 
+function initialize!(record::Record) #TODO: deprecate.
+    return empty!(record)
+end
+
 function checkfilled(record::Record)
     if !isfilled(record)
         throw(ArgumentError("unfilled SAM record"))

test/runtests.jl

@@ -196,6 +196,29 @@ end
             end
         end
     end
+
+    @testset "In-Place-Reading Pattern" begin
+
+        file_sam = joinpath(samdir, "ce#5b.sam")
+
+        records = open(collect, SAM.Reader, file_sam)
+
+        reader = open(SAM.Reader, file_sam)
+        record = SAM.Record()
+        i = 0
+        while !eof(reader)
+            empty!(record) # Reset the record.
+            read!(reader, record)
+
+            i = i + 1
+
+            @test records[i] == record
+
+        end
+
+        close(reader)
+
+    end
 end
 
 @testset "BAM" begin
@@ -414,6 +437,27 @@ end
         end
     end
 
+    @testset "In-Place-Reading Pattern" begin
+
+        file_bam = joinpath(bamdir, "ce#5b.bam")
+
+        records = open(collect, BAM.Reader, file_bam)
+
+        reader = open(BAM.Reader, file_bam)
+        record = BAM.Record()
+        i = 0
+        while !eof(reader)
+            empty!(record) # Reset the record.
+            read!(reader, record)
+
+            i = i + 1
+            @test records[i] == record
+        end
+
+        close(reader)
+
+    end
+
     @testset "Random access" begin
         filepath = joinpath(bamdir, "GSE25840_GSM424320_GM06985_gencode_spliced.head.bam")
         reader = open(BAM.Reader, filepath, index=filepath * ".bai")