Merge pull request #38 from chungongyu/dev

dev

3rdparty/CMakeLists.txt

@@ -0,0 +1,5 @@
+add_library(3rdparty
+ bcr.h
+ bcr.c
+ )
+target_include_directories(3rdparty PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})

3rdparty/Makefile.am

@@ -2,3 +2,4 @@ noinst_LTLIBRARIES = lib3rdparty.la
 lib3rdparty_la_SOURCES = \
  bcr.c \
  bcr.h
+EXTRA_DIST=CMakeLists.txt

CMakeLists.txt

@@ -0,0 +1,28 @@
+cmake_minimum_required(VERSION 3.11)
+
+project(siga VERSION 0.10)
+
+set(PROJECT_URL "http:https://bioinfo.ict.ac.cn/siga")
+set(PACKAGE_BUGREPORT "[email protected]")
+
+set(CMAKE_CXX_STANDARD 11)
+list(APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake")
+
+find_package(Boost COMPONENTS filesystem iostreams program_options unit_test_framework REQUIRED)
+find_package(OpenMP QUIET)
+find_package(RapidJSON REQUIRED)
+
+find_package(PkgConfig REQUIRED)
+pkg_check_modules(LOG4CXX REQUIRED liblog4cxx>=0.10.0)
+pkg_check_modules(TCMalloc QUIET libtcmalloc>=2.1)
+
+find_program(HELP2MAN NAMES help2man)
+find_program(BUNDLE NAMES bundle)
+
+configure_file(siga.h.in config.h @ONLY)
+enable_testing()
+
+add_subdirectory(3rdparty)
+add_subdirectory(docs)
+add_subdirectory(src)
+add_subdirectory(test)

Makefile.am

@@ -1,2 +1,4 @@
 SUBDIRS=3rdparty benchmark docs examples m4 src test
-EXTRA_DIST=autogen.sh
+EXTRA_DIST=autogen.sh \
+ CMakeLists.txt \
+ siga.h.in

docs/CMakeLists.txt

@@ -0,0 +1,8 @@
+if(BUNDLE)
+ add_custom_target(html ALL
+ COMMAND ${CMAKE_COMMAND} -E copy_if_different ${CMAKE_CURRENT_SOURCE_DIR}/Gemfile ${CMAKE_CURRENT_BINARY_DIR}/Gemfile
+ COMMAND bundle install --path=vendor/bundle
+ COMMAND bundle exec jekyll build --source=${CMAKE_CURRENT_SOURCE_DIR} --layouts=${CMAKE_CURRENT_SOURCE_DIR}
+ DEPENDS siga
+ )
+endif(BUNDLE)

docs/Makefile.am

@@ -4,7 +4,8 @@ EXTRA_DIST=404.html \
  _config.yml \
  favicon.png \
  index.md \
- logo_with_text.png
+ logo_with_text.png \
+ CMakeLists.txt
 html-env:
  bundle install --path=vendor/bundle
 html-local: html-env

siga.h.in

@@ -0,0 +1,7 @@
+#cmakedefine OpenMP_FOUND
+
+#define PACKAGE "@PROJECT_NAME@"
+#define PACKAGE_NAME "@PROJECT_NAME@"
+#define PACKAGE_VERSION "@PROJECT_VERSION@"
+#define PACKAGE_URL "@PROJECT_URL@"
+#define PACKAGE_BUGREPORT "@PROJECT_BUGREPORT@"

src/CMakeLists.txt

@@ -0,0 +1,69 @@
+add_library(libsiga
+ alphabet.h
+ asqg.cpp
+ asqg.h
+ bigraph.cpp
+ bigraph.h
+ bigraph_search.cpp
+ bigraph_search.h
+ bigraph_visitors.cpp
+ bigraph_visitors.h
+ bwt.cpp
+ bwt.h
+ constant.h
+ correct_processor.cpp
+ correct_processor.h
+ coord.cpp
+ coord.h
+ fmindex.cpp
+ fmindex.h
+ kmerdistr.cpp
+ kmerdistr.h
+ kseq.cpp
+ kseq.h
+ mkqs.h
+ overlap_builder.cpp
+ overlap_builder.h
+ primer_screen.cpp
+ primer_screen.h
+ quality.h
+ reads.cpp
+ reads.h
+ rlstring.h
+ runner.h
+ sequence_process_framework.h
+ suffix_array.cpp
+ suffix_array.h
+ suffix_array_builder.cpp
+ suffix_array_builder.h
+ utils.cpp
+ utils.h
+ )
+target_include_directories(libsiga PUBLIC ${CMAKE_BINARY_DIR} ${LOG4CXX_CFLAGS})
+target_link_libraries(libsiga 3rdparty ${LOG4CXX_LDFLAGS} Boost::filesystem Boost::iostreams Boost::program_options)
+if(TCMalloc_FOUND)
+ target_include_directories(libsiga PUBLIC ${TCMalloc_CFLAGS})
+ target_link_libraries(libsiga ${TCMalloc_LDFLAGS})
+endif(TCMalloc_FOUND)
+
+add_executable(siga
+ assembler.cpp
+ correct.cpp
+ indexer.cpp
+ match.cpp
+ overlap.cpp
+ preprocess.cpp
+ preqc.cpp
+ rmdup.cpp
+ subgraph.cpp
+ main.cpp
+ )
+target_link_libraries(siga libsiga)
+target_include_directories(siga PRIVATE ${CMAKE_BINARY_DIR})
+
+if(HELP2MAN)
+ add_custom_target(man ALL
+ COMMAND help2man -o siga.1 $<TARGET_FILE:siga>
+ DEPENDS siga
+ )
+endif(HELP2MAN)

src/Makefile.am

@@ -88,5 +88,5 @@ else
 man_MANS=
 endif !HELP2MAN
 
-EXTRA_DIST=log4cxx.properties
-
+EXTRA_DIST=log4cxx.properties \
+ CMakeLists.txt

src/bigraph.cpp

@@ -90,19 +90,22 @@ Vertex::Vertex(const Id& id, const std::string& seq, bool contained, const std::
  c = std::stoi(item.substr(k + 1));
  }
  }
- auto it = _indexTbl.find(barcode);
- if (it != _indexTbl.end()) {
- it->second += c;
- } else {
- _indexTbl[barcode] = c;
- }
+ _indexTbl.insert(std::make_pair(barcode, c));
+ // auto it = _indexTbl.find(barcode);
+ // if (it != _indexTbl.end()) {
+ // it->second += c;
+ // } else {
+ // _indexTbl[barcode] = c;
+ // }
  }
  }
  {
  std::vector<std::string> vec;
  ASQG::tokenize(vec, ext, ',');
  for (const auto& item : vec) {
- _ext.push_back(item);
+ if (!item.empty()) {
+ _ext.push_back(item);
+ }
  }
  }
 }
@@ -149,12 +152,13 @@ void Vertex::merge(Edge* edge) {
 
  // Update the index/barcode table of vertex
  for (const auto& idx : edge->end()->_indexTbl) {
- auto it = _indexTbl.find(idx.first);
- if (it != _indexTbl.end()) {
- it->second += idx.second;
- } else {
- _indexTbl[idx.first] = idx.second;
- }
+ _indexTbl.insert(std::make_pair(idx.first, idx.second));
+ // auto it = _indexTbl.find(idx.first);
+ // if (it != _indexTbl.end()) {
+ // it->second += idx.second;
+ // } else {
+ // _indexTbl[idx.first] = idx.second;
+ // }
  }
 
  // Update the extension attributes

src/bigraph.h

@@ -111,7 +111,7 @@ typedef std::vector<Edge *> EdgePtrList;
 class Vertex {
  public:
  typedef std::string Id;
- typedef std::unordered_map<std::string, size_t> IndexTable;
+ typedef std::unordered_multimap<std::string, size_t> IndexTable;
  typedef std::vector<std::string> ExtList;
 
  Vertex(const Id& id, const std::string& seq, bool contained=false, const std::string& index="", size_t coverage=1, const std::string& ext="");

src/kseq.cpp

@@ -132,6 +132,7 @@ DNASeqReader* DNASeqReaderFactory::create(std::istream& stream) {
  } else if (c == '>') {
  return new FASTAReader(stream);
  }
+ LOG4CXX_ERROR(logger, boost::format("failed to create dna reader: %c") % c);
  }
  return nullptr;
 }