[med-svn] [jellyfish] 01/10: Imported Upstream version 2.2.6

[Andreas Tille]

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tille pushed a commit to branch master
in repository jellyfish.

commit 7784a233d85edd8dda8627754a23d731527226b8
Author: Andreas Tille <tille at debian.org>
Date:   Tue Aug 30 13:36:04 2016 +0200

    Imported Upstream version 2.2.6
---
 configure.ac                                    | 2 +-
 include/jellyfish/rectangular_binary_matrix.hpp | 5 +++--
 jellyfish/merge_files.cc                        | 6 +++---
 sub_commands/count_main.cc                      | 2 +-
 swig/Makefile.am                                | 2 +-
 5 files changed, 9 insertions(+), 8 deletions(-)

diff --git a/configure.ac b/configure.ac
index 7515855..b4c1799 100644
--- a/configure.ac
+++ b/configure.ac
@@ -1,4 +1,4 @@
-AC_INIT([jellyfish], [2.2.5], [gmarcais at umd.edu])
+AC_INIT([jellyfish], [2.2.6], [gmarcais at umd.edu])
 AC_CANONICAL_HOST
 AC_CONFIG_MACRO_DIR([m4])
 AM_INIT_AUTOMAKE([subdir-objects foreign parallel-tests color-tests])
diff --git a/include/jellyfish/rectangular_binary_matrix.hpp b/include/jellyfish/rectangular_binary_matrix.hpp
index 75ab794..59b5103 100644
--- a/include/jellyfish/rectangular_binary_matrix.hpp
+++ b/include/jellyfish/rectangular_binary_matrix.hpp
@@ -344,9 +344,10 @@ namespace jellyfish {
         (((u128)1 << 64) - 1) << 64,
         ((u128)1 << 64) - 1,
         (u128)-1
-      };\
-    u128  res = res ^ res;
+      };
     u128* p   = (u128*)(_columns + _c - 2);
+    u128 res = 0;
+    //    u128  res = res ^ res;
 
     uint64_t j = 0, x = 0;
     for(unsigned int w = 0; w < nb_words(); ++w) {
diff --git a/jellyfish/merge_files.cc b/jellyfish/merge_files.cc
index 66fe517..bb57241 100644
--- a/jellyfish/merge_files.cc
+++ b/jellyfish/merge_files.cc
@@ -35,8 +35,8 @@ using jellyfish::file_header;
 using jellyfish::RectangularBinaryMatrix;
 using jellyfish::mer_dna;
 using jellyfish::cpp_array;
-typedef std::auto_ptr<binary_reader> binary_reader_ptr;
-typedef std::auto_ptr<text_reader> text_reader_ptr;
+typedef std::unique_ptr<binary_reader> binary_reader_ptr;
+typedef std::unique_ptr<text_reader> text_reader_ptr;
 
 struct file_info {
   std::ifstream is;
@@ -47,7 +47,7 @@ struct file_info {
   header(is)
   { }
 };
-typedef std::auto_ptr<RectangularBinaryMatrix> matrix_ptr;
+typedef std::unique_ptr<RectangularBinaryMatrix> matrix_ptr;
 
 template<typename reader_type, typename writer_type>
 void do_merge(cpp_array<file_info>& files, std::ostream& out, writer_type& writer,
diff --git a/sub_commands/count_main.cc b/sub_commands/count_main.cc
index cdfc7f4..20285e0 100644
--- a/sub_commands/count_main.cc
+++ b/sub_commands/count_main.cc
@@ -245,7 +245,7 @@ int count_main(int argc, char *argv[])
   if(args.disk_flag)
     ary.do_size_doubling(false);
 
-  std::auto_ptr<jellyfish::dumper_t<mer_array> > dumper;
+  std::unique_ptr<jellyfish::dumper_t<mer_array> > dumper;
   if(args.text_flag)
     dumper.reset(new text_dumper(args.threads_arg, args.output_arg, &header));
   else
diff --git a/swig/Makefile.am b/swig/Makefile.am
index aaf32b8..ceb260f 100644
--- a/swig/Makefile.am
+++ b/swig/Makefile.am
@@ -9,7 +9,7 @@ swig_v_GEN_0 = @echo "  SWIG    " $@;
 %/swig_wrap.cpp: $(SWIG_SRC)
 	$(SWIG_V_GEN)$(SWIG) -$(notdir $*) -I$(srcdir)/../include -o $@ $<
 else
-%/swig_wrap.cc:
+%/swig_wrap.cpp:
 	@echo >&2 SWIG >= 3.x.x not found. Make sure it is install and rerun configure
 	@false
 endif

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