clang changes

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

Author: AdityaPandeyCN

src/ramcore/RAMNTupleView.cxx

@@ -3,7 +3,7 @@
 #include <cstdint>
 #include <cstring>
 #include <iostream>
-#include <limits>
+#include <limits> // NOLINT(misc-include-cleaner)
 #include <string>
 
 #include <ROOT/RNTuple.hxx>
@@ -182,3 +182,4 @@ Long64_t ramntupleview(const char *file, const char *query, bool cache, bool per
    std::cout << "Found " << static_cast<long long>(count) << " records in region " << (query ? query : "") << std::endl;
    return count;
 }
+

src/ramcore/SamToNTuple.cxx

@@ -2,6 +2,16 @@
 #include "ramcore/SamParser.h"
 #include "rntuple/RAMNTupleRecord.h"
 
+#include <cstdint>
+#include <map>
+#include <memory>
+#include <cstdio>
+#include <thread>
+#include <vector>
+#include <mutex>
+#include <algorithm>
+#include <unordered_set>
+
 #include <ROOT/RNTupleModel.hxx>
 #include <ROOT/RNTupleWriter.hxx>
 #include <ROOT/RNTupleWriteOptions.hxx>
@@ -13,16 +23,6 @@
 #include <TFile.h>
 #include <TROOT.h>
 
-#include <cstdint>
-#include <map>
-#include <memory>
-#include <cstdio>
-#include <thread>
-#include <vector>
-#include <mutex>
-#include <algorithm>
-#include <unordered_set>
-
 void samtoramntuple(const char *datafile,
                     const char *treefile,
                     bool index, bool split, bool cache,
@@ -301,3 +301,4 @@ void samtoramntuple_split_by_chromosome(const char *datafile, const char *output
       }
    }
 }
+

test/ramcoretests.cxx

@@ -9,6 +9,7 @@
 #include <cstdio>
 #include <cstdlib>
 #include <filesystem>
+#include <string>
 
 #include "../tools/ramview.cxx"
 
@@ -55,14 +56,17 @@ TEST_F(ramcoreTest, ConversionProducesEqualEntries) {
     const char *region = "chrM:1-100000000";
 
     testing::internal::CaptureStdout();
-    ramview(ttreeFile, region, /*cache=*/true, /*perfstats=*/false, nullptr);
-    std::string ramview_output = testing::internal::GetCapturedStdout();
+    ramview(ttreeFile, 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, nullptr);
-    std::string ramntupleview_output = testing::internal::GetCapturedStdout();
+    ramntupleview(rntupleFile, 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);
 }
+

tools/samtoramntuple.cxx

@@ -31,6 +31,7 @@ int main(int argc, char* argv[]) {
            do_split = true;
         } else if (arg == "-only") {
            if (i + 1 < argc) {
+            
               only_chromosomes.emplace_back(argv[++i]);
            } else {
               std::cerr << "-only expects a chromosome name\n";