addressing clang comments

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>
+#include <memory> // NOLINT(misc-include-cleaner) - used for std::unique_ptr
 #include <mutex>
 #include <string>
-#include <thread>
-#include <unordered_set>
-#include <vector>
+#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 <ROOT/RNTupleModel.hxx>
 #include <ROOT/RNTupleWriter.hxx>
@@ -24,9 +24,9 @@
 #include <TFile.h>
 #include <TROOT.h>
 
-void samtoramntuple(const char *datafile, const char *treefile, bool index, bool split,
-                    bool cache, // NOLINT(misc-use-internal-linkage)
-                    int compression_algorithm, uint32_t quality_policy)
+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)
 {
    (void)split;
    (void)cache;

test/ramcoretests.cxx

@@ -15,7 +15,7 @@
 
 class ramcoreTest : public ::testing::Test {
 protected:
-   void SetUp() override
+   void SetUp() override // NOLINT(readability-convert-member-functions-to-static) - virtual method in Google Test
    {
       const int num_reads_for_test = 100;
       GenerateSAMFile("samexample.sam", num_reads_for_test);
@@ -24,14 +24,14 @@ class ramcoreTest : public ::testing::Test {
       std::remove("test_rntuple.root");
    }
 
-   void TearDown() override
+   void TearDown() override // NOLINT(readability-convert-member-functions-to-static) - virtual method in Google Test
    {
       std::remove("test_ttree.root");
       std::remove("test_rntuple.root");
    }
 };
 
-TEST_F(ramcoreTest, ConversionProducesEqualEntries)
+TEST_F(ramcoreTest, ConversionProducesEqualEntries) // NOLINT(misc-use-internal-linkage) - TEST_F is a macro
 {
    const char *samFile = "samexample.sam";
    const char *ttreeFile = "test_ttree.root";
@@ -59,13 +59,11 @@ TEST_F(ramcoreTest, ConversionProducesEqualEntries)
 
    testing::internal::CaptureStdout();
    ramview(ttreeFile, region, /*cache=*/true, /*perfstats=*/false, /*perfstatsfilename=*/nullptr);
-   std::string ramview_output;
-   ramview_output = testing::internal::GetCapturedStdout();
+   std::string ramview_output = testing::internal::GetCapturedStdout();
 
    testing::internal::CaptureStdout();
    ramntupleview(rntupleFile, region, /*cache=*/true, /*perfstats=*/false, /*perfstatsfilename=*/nullptr);
-   std::string ramntupleview_output;
-   ramntupleview_output = testing::internal::GetCapturedStdout();
+   std::string ramntupleview_output = testing::internal::GetCapturedStdout();
 
    EXPECT_TRUE(ramview_output.find("Found") != std::string::npos);
    EXPECT_TRUE(ramntupleview_output.find("Found") != std::string::npos);

tools/samtoramntuple.cxx

@@ -1,5 +1,6 @@
 #include "ramcore/SamToNTuple.h"
 #include "rntuple/RAMNTupleRecord.h"
+#include <exception>
 #include <iostream>
 #include <string>
 #include <cstring>
@@ -8,7 +9,8 @@
 int main(int argc, char *argv[])
 {
    if (argc < 2) {
-      std::cout << "Usage: " << argv[0] << " <input.sam> [output]\n";
+      std::cout << "Usage: " << argv[0]
+                << " <input.sam> [output]\n"; // NOLINT(cppcoreguidelines-pro-bounds-pointer-arithmetic)
       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";
@@ -18,7 +20,7 @@ int main(int argc, char *argv[])
       return 1;
    }
 
-   const char *input = argv[1];
+   const char *input = argv[1]; // NOLINT(cppcoreguidelines-pro-bounds-pointer-arithmetic)
    const char *output = nullptr;
 
    bool do_split = false;
@@ -27,13 +29,13 @@ int main(int argc, char *argv[])
    std::vector<std::string> only_chromosomes;
 
    for (int i = 2; i < argc; i++) {
-      std::string arg = argv[i];
+      std::string arg = argv[i]; // NOLINT(cppcoreguidelines-pro-bounds-pointer-arithmetic)
       if (arg == "-split") {
          do_split = true;
       } else if (arg == "-only") {
          if (i + 1 < argc) {
 
-            only_chromosomes.emplace_back(argv[++i]);
+            only_chromosomes.emplace_back(argv[++i]); // NOLINT(cppcoreguidelines-pro-bounds-pointer-arithmetic)
          } else {
             std::cerr << "-only expects a chromosome name\n";
             return 1;
@@ -42,14 +44,14 @@ int main(int argc, char *argv[])
          do_index = false;
       } else if (arg == "-illumina") {
          quality_mode = RAMNTupleRecord::kIlluminaBinning;
-      } else if (arg == "-dropqual") {
+      } else if (arg == "-dropqual") { // NOLINT(bugprone-branch-clone) - different values assigned
          quality_mode = RAMNTupleRecord::kDrop;
       } else if (arg[0] != '-') {
-         output = argv[i];
+         output = argv[i]; // NOLINT(cppcoreguidelines-pro-bounds-pointer-arithmetic)
       }
    }
 
-   std::string outfile;
+   std::string outfile{};
    if (!output) {
       outfile = std::string(input);
       size_t pos = outfile.rfind(".sam");