Merge pull request #19 from karel-brinda/logupdates

Ococo 0.1.2

.clang-format

@@ -0,0 +1,9 @@
+BasedOnStyle: Google
+Language: Cpp
+Standard: Cpp11
+AlignConsecutiveAssignments: true
+SortIncludes: true
+UseTab: Never
+IndentWidth: 4
+IndentCaseLabels: true
+NamespaceIndentation: None

.gitignore

@@ -1,25 +1,14 @@
 ococo
-ococo16
-ococo32
-a.fa
-
-Debug/
 
+.vscode/.*
 *~
-
+*.swp
 *.anjuta
 .anjuta*
 
 CTestTestfile.cmake
 Testing
 
-CMakeCache.txt
-CMakeFiles
-CMakeScripts
-Makefile
-cmake_install.cmake
-install_manifest.txt
-
 # Compiled Object files
 *.slo
 *.lo

.travis.yml

@@ -3,55 +3,32 @@ language: cpp
 cache:
   apt: true
 
-env:
-  global:
-    # Maintenance note: to move to a new version
-    # of boost, update both BOOST_ROOT and BOOST_URL.
-    # Note that for simplicity, BOOST_ROOT's final
-    # namepart must match the folder name internal
-    # to boost's .tar.gz.
-    - BOOST_ROOT=$HOME/boost_1_60_0
-    - BOOST_URL='http://downloads.sourceforge.net/project/boost/boost/1.60.0/boost_1_60_0.tar.gz?r=https%3A%2F%2Fsourceforge.net%2Fprojects%2Fboost%2Ffiles%2Fboost%2F1.60.0%2Fboost_1_60_0.tar.gz&ts=1460417589&use_mirror=netix'
-
 matrix:
   include:
 
     - os: linux 
       compiler: gcc
-      addons:
-        apt:
-          sources: ['ubuntu-toolchain-r-test', 'george-edison55-precise-backports']
-          packages: ['cmake', 'cmake-data']
       install:
         - sudo add-apt-repository ppa:ubuntu-toolchain-r/test -y
         - sudo add-apt-repository ppa:duggan/bats -y
         - sudo apt-get update
-        - sudo apt-get install g++-4.8 cmake zlib1g-dev git-svn bats libgtest-dev
+        - sudo apt-get install g++-4.8 zlib1g-dev bats
         - sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-4.8 90
         - sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.8 90
-        - ./scripts/install-boost.sh
-        - cd /usr/src/gtest && sudo cmake . && sudo cmake --build . && sudo mv libg* /usr/local/lib/ ; cd -
       script:
-        - cmake . -DBUILD_TESTS=1 && make && ./run.sh
-        - (cd tests/integration_tests && bats ${CI:+--tap} integration_tests.bats)
-        - ./tests/unit_tests/unittests
+        - make -j && ./run.sh
+        - (cd tests && bats ${CI:+--tap} tests.bats)
 
     - os: osx
       compiler: clang-3.7
       before_install:
         - sudo brew update
         - sudo brew tap homebrew/versions
         - sudo brew install llvm37
-        - sudo brew install boost155
         - sudo brew install bats
-        - sudo brew unlink cmake && sudo brew install cmake31
-        - sudo pip install --upgrade jinja2 nose
       install:
         - export CXX="clang++-3.7" CC="clang-3.7"
       script:
-        - cmake . && make && ./run.sh
-        - (cd tests/integration_tests && bats ${CI:+--tap} integration_tests.bats)
-
-cache:
-  directories:
-  - $BOOST_ROOT
+        - make -j  && ./run.sh
+        - (cd tests && bats ${CI:+--tap} tests.bats)
+

.vscode/c_cpp_properties.json

@@ -0,0 +1,33 @@
+{
+    "configurations": [
+        {
+            "name": "Mac",
+            "includePath": ["/usr/include"],
+            "browse" : {
+                "limitSymbolsToIncludedHeaders" : true,
+                "databaseFilename" : ""
+            }
+        },
+        {
+            "name": "Linux",
+            "includePath": ["/usr/include"],
+            "browse" : {
+                "limitSymbolsToIncludedHeaders" : true,
+                "databaseFilename" : ""
+            }
+        },
+        {
+            "name": "Win32",
+            "includePath": ["c:/Program Files (x86)/Microsoft Visual Studio 14.0/VC/include"],
+            "browse" : {
+                "limitSymbolsToIncludedHeaders" : true,
+                "databaseFilename" : ""
+            }
+        }
+    ],
+    "clang_format" : {
+        "style" : "file",
+        "fallback-style" : "LLVM",
+        "sort-includes" : false
+    }
+}

.vscode/settings.json

@@ -0,0 +1,4 @@
+// Place your settings in this file to overwrite default and user settings.
+{
+	"editor.tabSize": 4
+}

.vscode/tasks.json

@@ -0,0 +1,9 @@
+{
+    // See https://go.microsoft.com/fwlink/?LinkId=733558
+    // for the documentation about the tasks.json format
+    "version": "0.1.0",
+    "command": "make",
+    "isShellCommand": true,
+    "args": [],
+    "showOutput": "always"
+}

Makefile

@@ -0,0 +1,33 @@
+CXX      ?= g++
+CXXFLAGS = -std=c++11 -Wall -Wextra -Wno-missing-field-initializers -Wshadow -g -O2
+LIBS     = -lm -lz -lpthread
+
+PREFIX  = $(DESTDIR)/usr/local
+BINDIR  = $(PREFIX)/bin
+MANDIR  = $(PREFIX)/share/man/man1
+MANPAGE = ococo.1
+
+export CXX
+export CXXFLAGS
+
+.PHONY: all clean install ococo
+
+all: ococo
+
+install: ococo
+	install  ococo $(BINDIR)/ococo
+	install  $(MANPAGE) $(MANDIR)/$(MANPAGE)
+
+ococo:
+	$(MAKE) -C ./ext/htslib lib-static
+	$(MAKE) -C ./src
+
+	$(CXX) $(CXXFLAGS) $(DFLAGS) ./src/*.o -o $@ -L. $(LIBS) ./ext/htslib/libhts.a
+
+ext/htslib/libhts.a:
+	$(MAKE) -C ext/htslib lib-static
+
+clean:
+	$(MAKE) -C ext/htslib clean
+	$(MAKE) -C src clean
+	rm ococo