Add region query benchmark

benchmark/CMakeLists.txt

@@ -9,8 +9,19 @@ target_include_directories(sam_generator PUBLIC
     ${CMAKE_CURRENT_SOURCE_DIR}
 )
 
-target_link_libraries(sam_generator PRIVATE benchmark::benchmark)
-add_dependencies(sam_generator benchmark::benchmark)
+target_link_libraries(sam_generator PRIVATE 
+    benchmark::benchmark
+)
+
+add_library(ramtools_views STATIC
+    ${CMAKE_SOURCE_DIR}/tools/ramview.cxx
+    ${CMAKE_SOURCE_DIR}/tools/ramntupleview.cxx
+)
+
+target_link_libraries(ramtools_views PRIVATE 
+    ramcore 
+    ROOT::TreePlayer
+)
 
 ROOT_EXECUTABLE(sam_to_ram_benchmark
     sam_to_ram_benchmark.cxx
@@ -28,14 +39,30 @@ ROOT_EXECUTABLE(conversion_time_benchmark
         sam_generator
 )
 
-install(TARGETS sam_to_ram_benchmark conversion_time_benchmark
+ROOT_EXECUTABLE(region_query_benchmark
+    region_query_benchmark.cxx
+    LIBRARIES
+        benchmark::benchmark
+        ramcore
+        sam_generator
+        ramtools_views
+)
+
+install(TARGETS sam_to_ram_benchmark conversion_time_benchmark region_query_benchmark
     RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
 )
 
 add_custom_target(benchmark
+    COMMAND ${CMAKE_COMMAND} -E echo "=== SAM to RAM Benchmark ==="
     COMMAND sam_to_ram_benchmark
+    COMMAND ${CMAKE_COMMAND} -E echo ""
+    COMMAND ${CMAKE_COMMAND} -E echo "=== Conversion Time Benchmark ==="
     COMMAND conversion_time_benchmark
-    DEPENDS sam_to_ram_benchmark conversion_time_benchmark
+    COMMAND ${CMAKE_COMMAND} -E echo ""
+    COMMAND ${CMAKE_COMMAND} -E echo "=== Region Query Benchmark ==="
+    COMMAND region_query_benchmark
+    DEPENDS sam_to_ram_benchmark conversion_time_benchmark region_query_benchmark
     WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+    COMMENT "Running all RAM tools benchmarks"
 )
 

benchmark/benchmark_utils.h

@@ -0,0 +1,7 @@
+#pragma once
+
+#ifdef _WIN32
+#define NULL_DEVICE "NUL"
+#else
+#define NULL_DEVICE "/dev/null"
+#endif

benchmark/region_query_benchmark.cxx

@@ -0,0 +1,86 @@
+#include <benchmark/benchmark.h>
+#include "generate_sam_benchmark.h"
+#include "benchmark_utils.h"
+#include "ramcore/SamToTTree.h"
+#include "ramcore/SamToNTuple.h"
+#include <string>
+#include <cstdio>
+
+void ramview(const char *file, const char *query, bool cache = true, bool perfstats = false,
+             const char *perfstatsfilename = "perf.root");
+void ramntupleview(const char *file, const char *query, bool cache = true, bool perfstats = false,
+                   const char *perfstatsfilename = "perf.root");
+
+class RegionQueryFixture : public benchmark::Fixture {
+public:
+   void SetUp(const benchmark::State &state) override
+   {
+      num_reads_ = static_cast<int>(state.range(0));
+      sam_file_ = "region_query_test_" + std::to_string(num_reads_) + ".sam";
+
+      GenerateSAMFile(sam_file_, num_reads_);
+   }
+
+   void TearDown(const benchmark::State &) override { std::remove(sam_file_.c_str()); }
+
+protected:
+   int num_reads_;
+   std::string sam_file_;
+   static constexpr const char *region_ = "chr1:1-100000000";
+
+   void suppress_output() { freopen(NULL_DEVICE, "w", stdout); }
+
+   void restore_output() { freopen("/dev/tty", "w", stdout); }
+};
+
+BENCHMARK_DEFINE_F(RegionQueryFixture, TTree)(benchmark::State &state)
+{
+   std::string root_file = "ttree_" + std::to_string(num_reads_) + ".root";
+
+   suppress_output();
+   samtoram(sam_file_.c_str(), root_file.c_str(), true, true, true, 1, 0);
+   restore_output();
+
+   for (auto _ : state) {
+      suppress_output();
+      ramview(root_file.c_str(), region_, true, false, "perf.root");
+      restore_output();
+   }
+
+   std::remove(root_file.c_str());
+
+   state.counters["reads_per_sec"] = benchmark::Counter(num_reads_, benchmark::Counter::kIsRate);
+}
+
+BENCHMARK_DEFINE_F(RegionQueryFixture, RNTuple)(benchmark::State &state)
+{
+   std::string root_file = "rntuple_" + std::to_string(num_reads_) + ".root";
+
+   suppress_output();
+   samtoramntuple(sam_file_.c_str(), root_file.c_str(), true, true, true, 505, 0);
+   restore_output();
+
+   for (auto _ : state) {
+      suppress_output();
+      ramntupleview(root_file.c_str(), region_, true, false, "perf.root");
+      restore_output();
+   }
+
+   std::remove(root_file.c_str());
+
+   state.counters["reads_per_sec"] = benchmark::Counter(num_reads_, benchmark::Counter::kIsRate);
+}
+
+BENCHMARK_REGISTER_F(RegionQueryFixture, TTree)
+   ->Args({1000})
+   ->Args({10000})
+   ->Args({100000})
+   ->Unit(benchmark::kMillisecond);
+
+BENCHMARK_REGISTER_F(RegionQueryFixture, RNTuple)
+   ->Args({1000})
+   ->Args({10000})
+   ->Args({100000})
+   ->Unit(benchmark::kMillisecond);
+
+BENCHMARK_MAIN();

benchmark/sam_to_ram_benchmark.cxx

@@ -1,18 +1,13 @@
 #include <benchmark/benchmark.h>
 #include "generate_sam_benchmark.h"
+#include "benchmark_utils.h"
 #include "ramcore/SamToTTree.h"
 #include "ramcore/SamToNTuple.h"
 #include <filesystem>
 #include <iostream>
 #include <cstdio>
 #include <cstring>
 
-#ifdef _WIN32
-#define NULL_DEVICE "NUL"
-#else
-#define NULL_DEVICE "/dev/null"
-#endif
-
 static void BM_SamToRamComparison(benchmark::State &state)
 {
    int num_reads = state.range(0);