Add fast each_record method

lib/parse_fasta/fastq_file.rb

@@ -96,4 +96,39 @@ def each_record
     f.close if f.instance_of?(Zlib::GzipReader)
     return f
   end
+
+  def each_record_fast
+    count = 0
+    header = ''
+    sequence = ''
+    description = ''
+    quality = ''
+
+    begin
+      f = Zlib::GzipReader.open(self)
+    rescue Zlib::GzipFile::Error => e
+      f = self
+    end
+
+    f.each_line do |line|
+      line.chomp!
+
+      case count % 4
+      when 0
+        header = line[1..-1]
+      when 1
+        sequence = line
+      when 2
+        description = line[1..-1]
+      when 3
+        quality = line
+        yield(header, sequence, description, quality)
+      end
+
+      count += 1
+    end
+
+    f.close if f.instance_of?(Zlib::GzipReader)
+    return f
+  end
 end

spec/lib/fastq_file_spec.rb

@@ -21,7 +21,14 @@
 describe FastqFile do
   let(:records) {
     [["seq1", "AACCTTGG", "", ")#3gTqN8"],
-     ["seq2 apples", "ACTG", "seq2 apples", "*ujM"]] }
+     ["seq2 apples", "ACTG", "seq2 apples", "*ujM"]]
+  }
+
+  let(:records_fast) {
+    [["seq1", "AA CC TT GG", "", ")# 3g Tq N8"],
+     ["seq2 apples", "ACTG", "seq2 apples", "*ujM"]]
+  }
+
   let(:f_handle) { FastqFile.open(@fname).each_record { |s| } }
 
 
@@ -45,6 +52,27 @@
     end
   end
 
+  describe "#each_record_fast" do
+    before(:each) do
+      @fname = "#{File.dirname(__FILE__)}/../../test_files/test.fq.gz"
+    end
+
+    it "yields proper header, sequence, description, and quality" do
+      expect { |b|
+        FastqFile.open(@fname).each_record_fast(&b)
+      }.to yield_successive_args(records_fast[0], records_fast[1])
+    end
+
+    it "yields all params as String" do
+      FastqFile.open(@fname).each_record_fast do |h, s, d, q|
+        expect(h).to be_an_instance_of String
+        expect(s).to be_an_instance_of String
+        expect(d).to be_an_instance_of String
+        expect(q).to be_an_instance_of String
+      end
+    end
+  end
+
   describe "#to_hash" do
     let(:records) {
       { "seq1" => { head: "seq1",