tophat 2.0.6

- Upgrade to 2.0.6
- Add a patch: intializes variable length arrays to 1 for clang.
- Patch stops a variable length array non-POD element type error.
- Patch reported upstream via email and noted in comments.
- Add an LDFLAG for `-lboost_system-mt` because autoconf doesn't.
- Add a dep on boost because the build requires it and samtools.
- Works with superenv on ML with XCode-4.5.1.

Closes Homebrew/homebrew#15716.

Signed-off-by: Adam Vandenberg <flangy@gmail.com>

Formula/tophat.rb

@@ -1,28 +1,84 @@
 require 'formula'
 
 class Tophat < Formula
-  url 'http://tophat.cbcb.umd.edu/downloads/tophat-1.4.1.tar.gz'
   homepage 'http://tophat.cbcb.umd.edu/'
-  sha1 '0513bbcadb7194f12fbddeb3e4033e032f2fb29f'
+  url 'http://tophat.cbcb.umd.edu/downloads/tophat-2.0.6.tar.gz'
+  sha1 'd1c19cdccb5ddf74b8cb604a0ed1e5d33a25aae9'
 
   depends_on 'samtools'
+  depends_on 'boost'
 
-  fails_with :clang do
-    build 421
-    cause <<-EOS.undent
-      Compiling with clang results in the error "default arguments
-      cannot be added to a function template that has already been declared".
-      Upstream source should move default parameter declaration to fix.
-    EOS
-  end
+  # Variable length arrays using non-POD element types. Initialize with length=1
+  # Reported upstream via email to tophat-cufflinks@gmail.com on 28OCT2012
+  def patches; DATA; end
 
   def install
-    # It seems this project Makefile doesn't like -j4
-    # Disable until consult with upstream
+    # This can only build serially, otherwise it errors with no make target.
     ENV.deparallelize
 
-    system "./configure", "--disable-debug", "--disable-dependency-tracking",
+    # Must add this to fix missing boost symbols. Autoconf doesn't include it.
+    ENV.append 'LDFLAGS', '-lboost_system-mt'
+
+    system "./configure", "--disable-dependency-tracking",
                           "--prefix=#{prefix}"
     system "make install"
   end
 end
+
+__END__
+--- a/src/segment_juncs.cpp	2012-10-17 09:29:03.000000000 -0700
++++ b/src/segment_juncs.cpp	2012-10-27 22:24:44.000000000 -0700
+@@ -4854,15 +4854,15 @@
+       exit(0);
+     }
+
+-  std::set<Junction, skip_count_lt> vseg_juncs[num_threads];
++  std::set<Junction, skip_count_lt> vseg_juncs[1];
+   std::set<Junction, skip_count_lt> cov_juncs;
+   std::set<Junction, skip_count_lt> butterfly_juncs;
+
+   std::set<Junction> juncs;
+
+-  std::set<Deletion> vdeletions[num_threads];
+-  std::set<Insertion> vinsertions[num_threads];
+-  FusionSimpleSet vfusions[num_threads];
++  std::set<Deletion> vdeletions[1];
++  std::set<Insertion> vinsertions[1];
++  FusionSimpleSet vfusions[1];
+
+   RefSequenceTable rt(sam_header, true);
+
+--- a/src/tophat_reports.cpp	2012-10-18 10:43:09.000000000 -0700
++++ b/src/tophat_reports.cpp	2012-10-27 22:39:31.000000000 -0700
+@@ -2290,11 +2290,11 @@
+	num_threads = 1;
+     }
+
+-  JunctionSet vjunctions[num_threads];
+-  InsertionSet vinsertions[num_threads];
+-  DeletionSet vdeletions[num_threads];
+-  FusionSet vfusions[num_threads];
+-  Coverage vcoverages[num_threads];
++  JunctionSet vjunctions[1];
++  InsertionSet vinsertions[1];
++  DeletionSet vdeletions[1];
++  FusionSet vfusions[1];
++  Coverage vcoverages[1];
+
+   vector<boost::thread*> threads;
+   for (int i = 0; i < num_threads; ++i)
+@@ -2420,10 +2420,10 @@
+     fprintf(stderr, "Warning: %lu small overhang junctions!\n", (long unsigned int)small_overhangs);
+   */
+
+-  JunctionSet vfinal_junctions[num_threads];
+-  InsertionSet vfinal_insertions[num_threads];
+-  DeletionSet vfinal_deletions[num_threads];
+-  FusionSet vfinal_fusions[num_threads];
++  JunctionSet vfinal_junctions[1];
++  InsertionSet vfinal_insertions[1];
++  DeletionSet vfinal_deletions[1];
++  FusionSet vfinal_fusions[1];
+
+   for (int i = 0; i < num_threads; ++i)
+     {