clang changes

Signed-off-by: AdityaPandeyCN <adityapand3y666@gmail.com>

Author: AdityaPandeyCN

src/ramcore/SamToNTuple.cxx

@@ -6,12 +6,12 @@
 #include <cstdint>
 #include <cstdio>
 #include <map>
-#include <memory> // NOLINT(misc-include-cleaner) - used for std::unique_ptr
+#include <memory>
 #include <mutex>
 #include <string>
-#include <thread>        // NOLINT(misc-include-cleaner) - used for std::thread
-#include <unordered_set> // NOLINT(misc-include-cleaner) - used for std::unordered_set
-#include <vector>        // NOLINT(misc-include-cleaner) - used for std::vector
+#include <thread>
+#include <unordered_set>
+#include <vector>
 
 #include <ROOT/RNTupleModel.hxx>
 #include <ROOT/RNTupleWriter.hxx>
@@ -25,8 +25,8 @@
 #include <TROOT.h>
 
 void samtoramntuple(const char *datafile, const char *treefile, bool index,
-                    bool split, // NOLINT(misc-use-internal-linkage) - public API function
-                    bool cache, int compression_algorithm, uint32_t quality_policy)
+                    bool split, bool cache, int compression_algorithm,
+                    uint32_t quality_policy) // NOLINT(misc-use-internal-linkage) - public API function
 {
    (void)split;
    (void)cache;
@@ -300,3 +300,4 @@ void samtoramntuple_split_by_chromosome(const char *datafile, const char *output
       }
    }
 }
+

test/ramcoretests.cxx

@@ -13,41 +13,43 @@
 
 #include "../tools/ramview.cxx"
 
+namespace {
+
 class ramcoreTest : public ::testing::Test {
 protected:
-   void SetUp() override // NOLINT(readability-convert-member-functions-to-static) - virtual method in Google Test
+   const int m_num_reads_for_test = 100;
+   const std::string m_samFile = "samexample.sam";
+   const std::string m_ttreeFile = "test_ttree.root";
+   const std::string m_rntupleFile = "test_rntuple.root";
+
+   void SetUp() override
    {
-      const int num_reads_for_test = 100;
-      GenerateSAMFile("samexample.sam", num_reads_for_test);
+      GenerateSAMFile(m_samFile.c_str(), m_num_reads_for_test);
 
-      std::remove("test_ttree.root");
-      std::remove("test_rntuple.root");
+      std::remove(m_ttreeFile.c_str());
+      std::remove(m_rntupleFile.c_str());
    }
 
-   void TearDown() override // NOLINT(readability-convert-member-functions-to-static) - virtual method in Google Test
+   void TearDown() override
    {
-      std::remove("test_ttree.root");
-      std::remove("test_rntuple.root");
+      std::remove(m_ttreeFile.c_str());
+      std::remove(m_rntupleFile.c_str());
    }
 };
 
-TEST_F(ramcoreTest, ConversionProducesEqualEntries) // NOLINT(misc-use-internal-linkage) - TEST_F is a macro
+TEST_F(ramcoreTest, ConversionProducesEqualEntries)
 {
-   const char *samFile = "samexample.sam";
-   const char *ttreeFile = "test_ttree.root";
-   const char *rntupleFile = "test_rntuple.root";
-
-   samtoram(samFile, ttreeFile, true, true, true, 1, 0);
-   samtoramntuple(samFile, rntupleFile, true, true, true, 505, 0);
+   samtoram(m_samFile.c_str(), m_ttreeFile.c_str(), true, true, true, 1, 0);
+   samtoramntuple(m_samFile.c_str(), m_rntupleFile.c_str(), true, true, true, 505, 0);
 
-   auto ft = std::unique_ptr<TFile>(TFile::Open(ttreeFile));
+   auto ft = std::unique_ptr<TFile>(TFile::Open(m_ttreeFile.c_str()));
    ASSERT_TRUE(ft && !ft->IsZombie()) << "Failed to open TTree file";
 
    auto ttree = dynamic_cast<TTree *>(ft->Get("RAM"));
    ASSERT_NE(ttree, nullptr) << "Failed to get TTree";
    Long64_t ttreeEntries = ttree->GetEntries();
 
-   auto reader = ROOT::RNTupleReader::Open("RAM", rntupleFile);
+   auto reader = ROOT::RNTupleReader::Open("RAM", m_rntupleFile.c_str());
    ASSERT_NE(reader, nullptr) << "Failed to open RNTuple";
    Long64_t rntupleEntries = reader->GetNEntries();
 
@@ -58,14 +60,19 @@ TEST_F(ramcoreTest, ConversionProducesEqualEntries) // NOLINT(misc-use-internal-
    const char *region = "chrM:1-100000000";
 
    testing::internal::CaptureStdout();
-   ramview(ttreeFile, region, /*cache=*/true, /*perfstats=*/false, /*perfstatsfilename=*/nullptr);
-   std::string ramview_output = testing::internal::GetCapturedStdout();
+   ramview(m_ttreeFile.c_str(), region, /*cache=*/true, /*perfstats=*/false, /*perfstatsfilename=*/nullptr);
+   std::string ramview_output{};
+   ramview_output = testing::internal::GetCapturedStdout();
 
    testing::internal::CaptureStdout();
-   ramntupleview(rntupleFile, region, /*cache=*/true, /*perfstats=*/false, /*perfstatsfilename=*/nullptr);
-   std::string ramntupleview_output = testing::internal::GetCapturedStdout();
+   ramntupleview(m_rntupleFile.c_str(), region, /*cache=*/true, /*perfstats=*/false, /*perfstatsfilename=*/nullptr);
+   std::string ramntupleview_output{};
+   ramntupleview_output = testing::internal::GetCapturedStdout();
 
    EXPECT_TRUE(ramview_output.find("Found") != std::string::npos);
    EXPECT_TRUE(ramntupleview_output.find("Found") != std::string::npos);
    EXPECT_TRUE(ramntupleview_output.find("records in region") != std::string::npos);
 }
+
+} // namespace
+

tools/samtoramntuple.cxx

@@ -1,16 +1,22 @@
 #include "ramcore/SamToNTuple.h"
 #include "rntuple/RAMNTupleRecord.h"
+#include <algorithm>
+#include <cstring>
 #include <exception>
 #include <iostream>
 #include <string>
-#include <cstring>
 #include <vector>
 
 int main(int argc, char *argv[])
 {
-   if (argc < 2) {
-      std::cout << "Usage: " << argv[0]
-                << " <input.sam> [output]\n"; // NOLINT(cppcoreguidelines-pro-bounds-pointer-arithmetic)
+   std::vector<std::string> args;
+   args.reserve(static_cast<size_t>(argc));
+   std::for_each_n(argv, static_cast<size_t>(argc),
+                   [&](char *arg) { args.emplace_back(arg); });
+
+   if (args.size() < 2) {
+      std::cout << "Usage: " << args[0]
+                << " <input.sam> [output]\n";
       std::cout << "Options:\n";
       std::cout << "  -split             Split by chromosome\n";
       std::cout << "  -only <chr>        When used with -split, emit only the specified chromosome (repeatable)\n";
@@ -20,34 +26,34 @@ int main(int argc, char *argv[])
       return 1;
    }
 
-   const char *input = argv[1]; // NOLINT(cppcoreguidelines-pro-bounds-pointer-arithmetic)
+   const char *input = args[1].c_str();
    const char *output = nullptr;
 
    bool do_split = false;
    bool do_index = true;
    uint32_t quality_mode = RAMNTupleRecord::kPhred33;
    std::vector<std::string> only_chromosomes;
 
-   for (int i = 2; i < argc; i++) {
-      std::string arg = argv[i]; // NOLINT(cppcoreguidelines-pro-bounds-pointer-arithmetic)
+   for (int i = 2; i < static_cast<int>(args.size()); i++) {
+      std::string arg = args[static_cast<size_t>(i)];
       if (arg == "-split") {
          do_split = true;
       } else if (arg == "-only") {
-         if (i + 1 < argc) {
+         if (i + 1 < static_cast<int>(args.size())) {
 
-            only_chromosomes.emplace_back(argv[++i]); // NOLINT(cppcoreguidelines-pro-bounds-pointer-arithmetic)
+            only_chromosomes.emplace_back(args[static_cast<size_t>(++i)]);
          } else {
             std::cerr << "-only expects a chromosome name\n";
             return 1;
          }
       } else if (arg == "-noindex") {
          do_index = false;
-      } else if (arg == "-illumina") {
-         quality_mode = RAMNTupleRecord::kIlluminaBinning;
-      } else if (arg == "-dropqual") { // NOLINT(bugprone-branch-clone) - different values assigned
-         quality_mode = RAMNTupleRecord::kDrop;
-      } else if (arg[0] != '-') {
-         output = argv[i]; // NOLINT(cppcoreguidelines-pro-bounds-pointer-arithmetic)
+      } else if (arg == "-illumina" || arg == "-dropqual") {
+         quality_mode = (arg == "-illumina")
+                           ? RAMNTupleRecord::kIlluminaBinning
+                           : RAMNTupleRecord::kDrop;
+      } else if (!arg.empty() && arg[0] != '-') {
+         output = args[static_cast<size_t>(i)].c_str();
       }
    }
 
@@ -78,3 +84,4 @@ int main(int argc, char *argv[])
 
    return 0;
 }
+