[med-svn] [jellyfish] 01/04: Imported Upstream version 2.2.3

Andreas Tille tille at debian.org
Fri Jul 3 17:32:16 UTC 2015


This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository jellyfish.

commit 5b596efc8dd00a1e2e6a0e8d06062c675e9635dc
Author: Andreas Tille <tille at debian.org>
Date:   Fri Jul 3 19:03:03 2015 +0200

    Imported Upstream version 2.2.3
---
 Makefile.am                             |  8 ++++----
 README.md                               | 10 ++++++----
 configure.ac                            |  2 +-
 development.mk                          |  8 ++++----
 gtest.mk                                |  4 ++--
 include/jellyfish/mer_qual_iterator.hpp |  2 +-
 6 files changed, 18 insertions(+), 16 deletions(-)

diff --git a/Makefile.am b/Makefile.am
index 40c3740..a31b91f 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -8,7 +8,7 @@ pkgconfigdir = $(libdir)/pkgconfig
 pkgconfig_DATA = jellyfish-2.0.pc
 
 AM_LDFLAGS = -lpthread # $(VALGRIND_LIBS)
-AM_CPPFLAGS = -Wall -Wnon-virtual-dtor -I$(top_srcdir) -I$(top_srcdir)/include -g -O3 $(VALGRIND_CFLAGS)
+AM_CPPFLAGS = -Wall -Wnon-virtual-dtor -I$(srcdir) -I$(srcdir)/include -g -O3 $(VALGRIND_CFLAGS)
 AM_CXXFLAGS = $(ALL_CXXFLAGS) -g -O3
 
 noinst_HEADERS = $(YAGGO_SOURCES)
@@ -136,7 +136,7 @@ YAGGO_SOURCES += jellyfish/generate_sequence_cmdline.hpp
 # Tests #
 #########
 TEST_EXTENSIONS = .sh
-SH_LOG_COMPILER = /bin/sh
+SH_LOG_COMPILER = $(SHELL)
 AM_SH_LOG_FLAGS =
 
 TESTS = tests/generate_sequence.sh tests/parallel_hashing.sh	\
@@ -204,13 +204,13 @@ bin_test_all_SOURCES = unit_tests/test_main.cc				\
 bin_test_all_SOURCES += jellyfish/backtrace.cc
 
 bin_test_all_CPPFLAGS = -Dprotected=public -Dprivate=public -DJSON_IS_AMALGAMATION=1
-bin_test_all_CXXFLAGS = $(AM_CXXFLAGS) -I$(top_srcdir)/unit_tests/gtest/include -I$(top_srcdir)/unit_tests -I$(top_srcdir)/include
+bin_test_all_CXXFLAGS = $(AM_CXXFLAGS) -I$(srcdir)/unit_tests/gtest/include -I$(srcdir)/unit_tests -I$(srcdir)/include
 bin_test_all_LDADD = libgtest.la $(LDADD)
 YAGGO_SOURCES += unit_tests/test_main_cmdline.hpp
 noinst_HEADERS += unit_tests/test_main.hpp
 
 include gtest.mk
--include $(top_srcdir)/development.mk
+-include $(srcdir)/development.mk
 
 # Print the value of a variable
 print-%:
diff --git a/README.md b/README.md
index 33fb499..8c8af70 100644
--- a/README.md
+++ b/README.md
@@ -15,7 +15,7 @@ If you use Jellyfish in your research, please cite:
 Installation
 ------------
 
-To get an easier to compiled packaged tar ball of the source code, see the [home page of Jellyfish at the University of Maryland][1].
+To get an easier to compiled packaged tar ball of the source code, download a release from [home page of Jellyfish at the University of Maryland][1] or from the [github release][3].
 
 To compile from the git tree, you will need autoconf/automake, make, g++ 4.4 or newer and [yaggo](https://github.com/gmarcais/yaggo "Yaggo on github"). Then compile with:
 
@@ -35,15 +35,15 @@ In the examples directory are potentially useful extra programs to query/manipul
 Binding to script languages
 ---------------------------
 
-Bindings to Ruby, Python and Perl are provided. This binding allows to read the output file of Jellyfish directly in a scripting language. Compilation of the bindings is easier from the tarball provided on [Jellyfish's home page][1].
+Bindings to Ruby, Python and Perl are provided. This binding allows to read the output file of Jellyfish directly in a scripting language. Compilation of the bindings is easier from the [release tarball][3]: [SWIG][2] is not required and in the command lines shown below, remove the `--enable-swig` switch. Only the development files of the scripting languages are required.
 
-Compilation of the bindings from the git tree requires [SWIG](http://swig.org) version 3, and the development files of the scripting languages. To compile all three bindings, configure with:
+Compilation of the bindings from the git tree requires [SWIG][2] version 3, and the development files of the scripting languages. To compile all three bindings, configure with:
 
 ```Shell
 ./configure --enable-swig --enable-ruby-binding --enable-python-binding --enable-perl-binding
 ```
 
-Note that the headers of older version of Perl 5 do not compile with recent compilers (g++ > 4.4, clang++) and C++11 mode enable. One may have to specify in addition `CXX=g++4.4` to compile the perl binding.
+Note that the headers of older version of Perl 5 do not compile with recent compilers (g++ > 4.4, clang++) and C++11 mode enable. One may have to specify the path to version 4.4 of gcc by adding, for example, `CXX=g++4.4` to the configure commande line.
 
 The binding can installed in a different location than the default (which may require root privileges for example) by passing a path to the `--enable` switches. Then, for Python, Ruby or Perl to find the binding, an environment variable may need to be adjusted (`PYTHONPATH`, `RUBYLIB` and `PERL5LIB` respectively). For example:
 
@@ -55,3 +55,5 @@ export PYTHONPATH=$HOME/lib/python
 See the `swig` directory for examples on how to use the bindings.
 
 [1]: http://www.genome.umd.edu/jellyfish.html "Genome group at University of Maryland"
+[2]: http://www.swig.org/
+[3]: https://github.com/gmarcais/Jellyfish/releases "Jellyfish release"
diff --git a/configure.ac b/configure.ac
index 9c6a865..575f8f2 100644
--- a/configure.ac
+++ b/configure.ac
@@ -1,4 +1,4 @@
-AC_INIT([jellyfish], [2.2.1], [gmarcais at umd.edu])
+AC_INIT([jellyfish], [2.2.3], [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/development.mk b/development.mk
index 7043903..9cd1e66 100644
--- a/development.mk
+++ b/development.mk
@@ -5,14 +5,14 @@ AM_CXXFLAGS += -Werror
 cloc:
 	cloc --force-lang="Ruby,yaggo" --force-lang="make,am" --force-lang="make,mk" \
 	  --exclude-dir="gtest" --ignored=cloc_ignored_src_files \
-	  $(top_srcdir)/jellyfish $(top_srcdir)/include $(top_srcdir)/lib $(top_srcdir)/sub_commands $(top_srcdir)/tests $(top_srcdir)/unit_tests \
-	  $(top_srcdir)/Makefile.am $(top_srcdir)/*.mk
+	  $(srcdir)/jellyfish $(srcdir)/include $(srcdir)/lib $(srcdir)/sub_commands $(srcdir)/tests $(srcdir)/unit_tests \
+	  $(srcdir)/Makefile.am $(srcdir)/*.mk
 
 cloc_jellyfish:
-	cloc $(top_srcdir)/jellyfish $(top_srcdir)/include $(top_srcdir)/lib $(top_srcdir)/sub_commands
+	cloc $(srcdir)/jellyfish $(srcdir)/include $(srcdir)/lib $(srcdir)/sub_commands
 
 cloc_library:
-	cloc $(top_srcdir)/include $(top_srcdir)/lib
+	cloc $(srcdir)/include $(srcdir)/lib
 
 # Make a dependency on yaggo the software
 $(YAGGO_SOURCES): $(YAGGO)
diff --git a/gtest.mk b/gtest.mk
index 9ae1440..f9d2168 100755
--- a/gtest.mk
+++ b/gtest.mk
@@ -7,8 +7,8 @@ check_LTLIBRARIES = libgtest.la libgtest_main.la
 libgtest_la_SOURCES = unit_tests/gtest/src/gtest-all.cc
 libgtest_main_la_SOURCES = unit_tests/gtest/src/gtest_main.cc
 libgtest_main_la_LIBADD = libgtest.la
-libgtest_la_CXXFLAGS = -I$(top_srcdir)/unit_tests
-libgtest_main_la_CXXFLAGS = -I$(top_srcdir)/unit_tests
+libgtest_la_CXXFLAGS = -I$(srcdir)/unit_tests
+libgtest_main_la_CXXFLAGS = -I$(srcdir)/unit_tests
 
 GTEST_SRC = unit_tests/gtest/src/gtest-all.cc	\
 	    unit_tests/gtest/src/gtest_main.cc	\
diff --git a/include/jellyfish/mer_qual_iterator.hpp b/include/jellyfish/mer_qual_iterator.hpp
index 3d7dbbc..328322d 100644
--- a/include/jellyfish/mer_qual_iterator.hpp
+++ b/include/jellyfish/mer_qual_iterator.hpp
@@ -81,7 +81,7 @@ public:
 
       do {
         const int  code = m_.code(*cseq_++);
-        const char qual = cqual_ < equal_ ? *cqual_++ : std::numeric_limits<char>::min();
+         const char qual = cqual_ < equal_ ? *cqual_++ : std::numeric_limits<char>::max();
         if(code >= 0 && qual >= min_qual_) {
           m_.shift_left(code);
           if(canonical_)

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