This is an automated email from the git hooks/post-receive script. tille pushed a commit to annotated tag upstream/2.2.3 in repository jellyfish1.
commit 5b596efc8dd00a1e2e6a0e8d06062c675e9635dc Author: Andreas Tille <[email protected]> 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], [[email protected]]) +AC_INIT([jellyfish], [2.2.3], [[email protected]]) 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_) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/jellyfish1.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
