From 7e8ba7c1388204daa5245d2128d01f6f40298185 Mon Sep 17 00:00:00 2001
From: Naohisa Goto <ng@bioruby.org>
Date: Thu, 18 Aug 2011 00:08:51 +0900
Subject: [PATCH] In Fastq formatter, default width value changed to nil

 * In Bio::Sequence#output(:fastq) (Fastq output formatter),
   default width value is changed from 70 to nil, which means
   "without wrapping".  close [Feature #3191]
   (https://redmine.open-bio.org/issues/3191)
---
 RELEASE_NOTES.rdoc               |  8 ++++++--
 lib/bio/db/fastq/format_fastq.rb |  4 ++--
 test/unit/bio/db/test_fastq.rb   | 12 ++++++++++++
 3 files changed, 20 insertions(+), 4 deletions(-)

diff --git a/RELEASE_NOTES.rdoc b/RELEASE_NOTES.rdoc
index 40111373d..8c31b0f6a 100644
--- a/RELEASE_NOTES.rdoc
+++ b/RELEASE_NOTES.rdoc
@@ -56,9 +56,13 @@ Google Summer of Code 2010.
 
 == Incompatible changes
 
-=== Bio::SPTR
+=== Bio::Sequence#output(:fastq)
 
-==== CC line topic "WEB RESOURCE"
+In Fastq output formatter, default width value is changed from 70 to nil.
+The nil means "without wrapping". The new default behavior without wrapping
+is generally good with many recent applications that read fastq.
+
+=== Bio::SPTR CC line topic "WEB RESOURCE"
 
 In the return value of Bio::SPTR#cc('WEB RESOURCE'), "NAME" and "NOTE"
 are now renamed to "Name" and "Note", respectively. The change is due to
diff --git a/lib/bio/db/fastq/format_fastq.rb b/lib/bio/db/fastq/format_fastq.rb
index 520b37a9c..10bf235c0 100644
--- a/lib/bio/db/fastq/format_fastq.rb
+++ b/lib/bio/db/fastq/format_fastq.rb
@@ -26,7 +26,7 @@ class Fastq < Bio::Sequence::Format::FormatterBase
     # *Arguments*:
     # * _sequence_: Bio::Sequence object
     # * (optional) :repeat_title => (true or false) if true, repeating title in the "+" line; if not true, "+" only (default false)
-    # * (optional) :width => _width_: (Fixnum) width to wrap sequence and quality lines;  nil to prevent wrapping (default 70)
+    # * (optional) :width => _width_: (Fixnum) width to wrap sequence and quality lines;  nil to prevent wrapping (default nil)
     # * (optional) :title => _title_: (String) completely replaces title line with the _title_ (default nil)
     # * (optional) :default_score => _score_: (Integer) default score for bases that have no valid quality scores or error probabilities; false or nil means the lowest score, true means the highest score (default nil)
     def initialize; end if false # dummy for RDoc
@@ -43,7 +43,7 @@ def initialize; end if false # dummy for RDoc
     # *Returns*:: String object
     def output
       title = @options[:title]
-      width = @options.has_key?(:width) ? @options[:width] : 70
+      width = @options.has_key?(:width) ? @options[:width] : nil
       seq = @sequence.seq.to_s
       entry_id = @sequence.entry_id || 
         "#{@sequence.primary_accession}.#{@sequence.sequence_version}"
diff --git a/test/unit/bio/db/test_fastq.rb b/test/unit/bio/db/test_fastq.rb
index 90c68f1f7..9e09ae66b 100644
--- a/test/unit/bio/db/test_fastq.rb
+++ b/test/unit/bio/db/test_fastq.rb
@@ -369,6 +369,18 @@ def test_to_biosequence
         end
       end
 
+      def test_to_biosequence_and_output
+        @ff.each_with_index do |e, i|
+          id_line = IDLINES[i]
+          seq_line = SEQS[i]
+          qual_line = QUALITY_STRINGS[i]
+          # Changed default width to nil (no wrapping)
+          expected = "@#{id_line}\n#{seq_line}\n+\n#{qual_line}\n"
+          actual = e.to_biosequence.output(:fastq_sanger)
+          assert_equal(expected, actual)
+        end
+      end
+
       def test_roundtrip
         @ff.each_with_index do |e, i|
           str_orig = @ff.entry_raw