[med-svn] [jellyfish1] 04/04: Imported Upstream version 2.2.3
Andreas Tille
tille at debian.org
Tue Nov 17 07:42:28 UTC 2015
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 <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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