Empty records during iteration

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

@@ -76,6 +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

@@ -571,7 +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
@@ -588,6 +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"))