Merge remote-tracking branch 'clara-parabricks/dev' into omosafi/support-calendar-versioning

Author: ohadmo

.gitmodules

@@ -33,3 +33,6 @@
 [submodule "3rdparty/htslib"]
 	path = 3rdparty/htslib
 	url = https://github.com/samtools/htslib.git
+[submodule "3rdparty/libcudacxx"]
+	path = 3rdparty/libcudacxx
+	url = https://github.com/NVIDIA/libcudacxx

3rdparty/libcudacxx

@@ -68,10 +68,10 @@ else()
     set_property(GLOBAL PROPERTY gw_library_type STATIC)
 endif()
 
-include(cmake/CXX.cmake)
 include(cmake/CUDA.cmake)
-include(cmake/Doxygen.cmake)
 include(cmake/3rdparty.cmake)
+include(cmake/CXX.cmake) # Must occur after 3rdparty modules are added
+include(cmake/Doxygen.cmake)
 include(cmake/Tests.cmake)
 include(cmake/Benchmarks.cmake)
 include(cmake/Format.cmake)

CMakeLists.txt

@@ -42,6 +42,10 @@ add_library(cub INTERFACE IMPORTED)
 #cmake before 3.11, use the following for now:
 set_property(TARGET cub APPEND PROPERTY INTERFACE_INCLUDE_DIRECTORIES "${CUB_DIR}")
 
+set(LIBCUDACXX_DIR ${PROJECT_SOURCE_DIR}/3rdparty/libcudacxx CACHE STRING "Path to libcu++ repo.")
+add_library(libcudacxx INTERFACE IMPORTED)
+set_property(TARGET libcudacxx APPEND PROPERTY INTERFACE_INCLUDE_DIRECTORIES "${LIBCUDACXX_DIR}/include")
+
 set(KSEQPP_DIR ${PROJECT_SOURCE_DIR}/3rdparty/kseqpp/src CACHE STRING
     "Path to kseqpp repo")
 

cmake/3rdparty.cmake

@@ -21,3 +21,6 @@ set(CMAKE_CXX_STANDARD 17)
 
 #Add OpenMP
 set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fopenmp")
+
+# Add common copmiler checks
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Werror -Wall -Wextra")

cmake/CXX.cmake

@@ -86,7 +86,7 @@ function(gw_enable_formatting_targets)
         endforeach()
 
         add_custom_target(format DEPENDS ${format_list} COMMENT "Format source files")
-        add_custom_target(check-format DEPENDS ${format_check_list} COMMENT "Check format of source files")
+        add_custom_target(check-format ALL DEPENDS ${format_check_list} COMMENT "Check format of source files")
     else()
         message(STATUS "clang-format not found. Auto-formatting disabled.")
     endif()

cmake/Format.cmake

@@ -105,7 +105,7 @@ class buffer
     buffer(buffer&& rhs)
         : data_(std::exchange(rhs.data_, nullptr))
         , size_(std::exchange(rhs.size_, 0))
-        , streams_(rhs.streams_)
+        , streams_(std::exchange(rhs.streams_, {}))
         , allocator_(rhs.allocator_)
     {
     }
@@ -116,9 +116,13 @@ class buffer
     /// \return refrence to this buffer.
     buffer& operator=(buffer&& rhs)
     {
+        if (nullptr != data_)
+        {
+            allocator_.deallocate(data_, size_);
+        }
         data_      = std::exchange(rhs.data_, nullptr);
         size_      = std::exchange(rhs.size_, 0);
-        streams_   = rhs.streams_;
+        streams_   = std::exchange(rhs.streams_, {});
         allocator_ = rhs.allocator_;
         return *this;
     }

common/base/include/claraparabricks/genomeworks/utils/device_buffer.hpp

@@ -143,16 +143,12 @@ inline std::vector<std::string> generate_random_sequences(std::string const& bac
 
 inline void reverse_complement(const char* src, const int32_t length, char* dest)
 {
+    // lookup for substitution: A -> T; C -> G; T -> A; G -> C.
+    constexpr char lookup[] = {'T', 'G', 'A', 'C'};
     for (int32_t pos = 0; pos < length; pos++)
     {
-        switch (char nucleotide = src[length - 1 - pos])
-        {
-        case 'A': dest[pos] = 'T'; break;
-        case 'T': dest[pos] = 'A'; break;
-        case 'C': dest[pos] = 'G'; break;
-        case 'G': dest[pos] = 'C'; break;
-        default: dest[pos] = nucleotide;
-        }
+        const unsigned char nucleotide = src[length - 1 - pos];
+        dest[pos]                      = lookup[(nucleotide >> 1) & 0x3];
     }
 }
 

common/base/include/claraparabricks/genomeworks/utils/genomeutils.hpp

@@ -26,6 +26,8 @@ namespace claraparabricks
 namespace genomeworks
 {
 #ifdef GW_CUDA_BEFORE_10_1
+#pragma GCC diagnostic push
+#pragma GCC diagnostic ignored "-Wignored-qualifiers"
 template <typename T>
 struct numeric_limits
 {
@@ -44,6 +46,7 @@ struct numeric_limits<int32_t>
     GW_CONSTEXPR static __device__ int32_t max() { return INT32_MAX; }
     GW_CONSTEXPR static __device__ int32_t min() { return INT32_MIN; }
 };
+#pragma GCC diagnostic pop
 #else
 using std::numeric_limits;
 #endif

common/base/include/claraparabricks/genomeworks/utils/limits.cuh

@@ -17,7 +17,10 @@
 #pragma once
 
 #include <vector>
+#pragma GCC diagnostic push
+#pragma GCC diagnostic ignored "-Wunused-parameter"
 #include <thrust/system/cuda/experimental/pinned_allocator.h>
+#pragma GCC diagnostic pop
 
 namespace claraparabricks
 {