Index Repairing of RNTuple ROOT file #13

AdityaPandeyCN · 2025-11-16T06:21:42Z

This PR addresses:-

RNTuple region query: columnar views (flag/refid/pos), zero-based ranges, CIGAR-span overlap, indexed start, early breaks and skip heuristic. Counts now match samtools; large-region throughput improved significantly.
TTree ramview: fixed 1-/0-based mismatch, added FLAG filter (0x904), refid gating, and early termination. Correct counts across regions.
Converter/index: index mapped reads only; hybrid sparse index (chromosome start, every 10kb, every 100 mapped reads). Reduced noisy output.
Chromosome split filter: support -split -only (repeatable) to emit specific chromosomes; wired into samtoramntuple_split_by_chromosome.
Benchmarks/docs: updated region suite and README with RNTuple vs. CRAM comparisons; explain why CRAM is faster on tiny windows and why RNTuple wins on broad regions.

github-actions

clang-tidy made some suggestions

There were too many comments to post at once. Showing the first 10 out of 24. Check the log or trigger a new build to see more.

github-actions · 2025-11-16T06:38:50Z

benchmark/generate_sam_benchmark.cxx

@@ -1,6 +1,6 @@
 #include <benchmark/benchmark.h>


warning: 'benchmark/benchmark.h' file not found [clang-diagnostic-error]

#include <benchmark/benchmark.h> ^

github-actions · 2025-11-16T06:38:50Z

benchmark/region_query_benchmark.cxx

-                                                               "chr21:1-48129895",
-                                                               "chrM:1-16571",
-                                                               "chrY:2600000-2700000",
+const std::vector<std::string> RegionQueryFixture::regions_ = {"1:1000000-1001000",


warning: invalid case style for variable 'regions_' [readability-identifier-naming]

Suggested change

const std::vector<std::string> RegionQueryFixture::regions_ = {"1:1000000-1001000",

const std::vector<std::string> RegionQueryFixture::regions = {"1:1000000-1001000",

github-actions · 2025-11-16T06:38:51Z

benchmark/region_query_benchmark.cxx

-BENCHMARK_REGISTER_F(RegionQueryFixture, TTree)->Args({0})->Args({3})->Args({6})->Args({9})->Unit(benchmark::kSecond);
-
-BENCHMARK_REGISTER_F(RegionQueryFixture, RNTuple)->Args({0})->Args({3})->Args({6})->Args({9})->Unit(benchmark::kSecond);
+BENCHMARK_REGISTER_F(RegionQueryFixture, TTree)->DenseRange(0, 17, 1)->Unit(benchmark::kSecond);


warning: function 'BENCHMARK_REGISTER_F' can be made static or moved into an anonymous namespace to enforce internal linkage [misc-use-internal-linkage]

Suggested change

BENCHMARK_REGISTER_F(RegionQueryFixture, TTree)->DenseRange(0, 17, 1)->Unit(benchmark::kSecond);

BENCHMARK_REGISTER_Fstatic (RegionQueryFixture, TTree)->DenseRange(0, 17, 1)->Unit(benchmark::kSecond);

github-actions · 2025-11-16T06:38:51Z

benchmark/region_query_benchmark.cxx

-
-BENCHMARK_REGISTER_F(RegionQueryFixture, RNTuple)->Args({0})->Args({3})->Args({6})->Args({9})->Unit(benchmark::kSecond);
+BENCHMARK_REGISTER_F(RegionQueryFixture, TTree)->DenseRange(0, 17, 1)->Unit(benchmark::kSecond);
+BENCHMARK_REGISTER_F(RegionQueryFixture, RNTuple)->DenseRange(0, 17, 1)->Unit(benchmark::kSecond);


warning: function 'BENCHMARK_REGISTER_F' can be made static or moved into an anonymous namespace to enforce internal linkage [misc-use-internal-linkage]

Suggested change

BENCHMARK_REGISTER_F(RegionQueryFixture, RNTuple)->DenseRange(0, 17, 1)->Unit(benchmark::kSecond);

BENCHMARK_REGISTER_Fstatic (RegionQueryFixture, RNTuple)->DenseRange(0, 17, 1)->Unit(benchmark::kSecond);

github-actions · 2025-11-16T06:38:51Z

inc/ramcore/SamToNTuple.h

 #ifndef RAMCORE_SAMTONTUPLE_H
 #define RAMCORE_SAMTONTUPLE_H

 #include <cstdint>


warning: 'cstdint' file not found [clang-diagnostic-error]

#include <cstdint> ^

github-actions · 2025-11-16T06:38:51Z

inc/ramcore/SamToNTuple.h

 void samtoramntuple_split_by_chromosome(const char *datafile, const char *output_prefix, int compression_algorithm,
-                                        uint32_t quality_policy, int num_threads = 4);
+                                        uint32_t quality_policy, int num_threads = 4,
+                                        const std::vector<std::string> &only_chromosomes = {});


warning: parameter 6 is const-qualified in the function declaration; const-qualification of parameters only has an effect in function definitions [readability-avoid-const-params-in-decls]

Suggested change

const std::vector<std::string> &only_chromosomes = {});

std::vector<std::string> &only_chromosomes = {});

github-actions · 2025-11-16T06:38:51Z

src/ramcore/RAMNTupleView.cxx

@@ -1,6 +1,7 @@
 #include "ramcore/RAMNTupleView.h"


warning: 'ramcore/RAMNTupleView.h' file not found [clang-diagnostic-error]

#include "ramcore/RAMNTupleView.h" ^

github-actions · 2025-11-16T06:38:51Z

src/ramcore/RAMNTupleView.cxx

 #include <iostream>
 #include <cstring>
+#include <limits>
 #include <ROOT/RNTuple.hxx>


warning: included header limits is not used directly [misc-include-cleaner]

Suggested change

#include <ROOT/RNTuple.hxx>

#include <ROOT/RNTuple.hxx>

github-actions · 2025-11-16T06:38:51Z

src/ramcore/RAMNTupleView.cxx

+      int rangeDelimiterPos = region.find("-", chrDelimiterPos);
+      if (rangeDelimiterPos == std::string::npos) {
+         try {
+            range_start = std::stoi(region.substr(chrDelimiterPos + 1));


warning: no header providing "std::stoi" is directly included [misc-include-cleaner]

range_start = std::stoi(region.substr(chrDelimiterPos + 1)); ^

github-actions · 2025-11-16T06:38:52Z

src/ramcore/RAMNTupleView.cxx

-
-   auto recordView = reader->GetView<RAMNTupleRecord>("record");
+   auto flagView = reader->GetView<uint16_t>("record.flag");
+   auto refidView = reader->GetView<int32_t>("record.refid");


warning: no header providing "int32_t" is directly included [misc-include-cleaner]

src/ramcore/RAMNTupleView.cxx:1:

- #include <iostream> + #include <cstdint> + #include <iostream>

github-actions

clang-tidy made some suggestions

There were too many comments to post at once. Showing the first 10 out of 17. Check the log or trigger a new build to see more.

github-actions · 2025-11-16T07:57:50Z

src/ramcore/RAMNTupleView.cxx

@@ -1,6 +1,9 @@
 #include "ramcore/RAMNTupleView.h"
+#include <cstdint>


warning: #includes are not sorted properly [llvm-include-order]

#include <cstdint> ^

this fix will not be applied because it overlaps with another fix

github-actions · 2025-11-16T07:57:50Z

src/ramcore/RAMNTupleView.cxx


   stopwatch.Print();
-
+   printf("Found %lld records in region %s\n", static_cast<long long>(count), query ? query : "");


warning: do not call c-style vararg functions [cppcoreguidelines-pro-type-vararg]

printf("Found %lld records in region %s\n", static_cast<long long>(count), query ? query : ""); ^

github-actions · 2025-11-16T07:57:51Z

src/ramcore/SamToNTuple.cxx

 #include <mutex>
 #include <algorithm>
+#include <unordered_set>



warning: included header unordered_set is not used directly [misc-include-cleaner]

Suggested change

github-actions · 2025-11-16T07:57:51Z

src/ramcore/SamToNTuple.cxx

+
+   auto rootFile = std::unique_ptr<TFile>(TFile::Open(treefile, "RECREATE"));
+   if (!rootFile || !rootFile->IsOpen()) {
+      printf("Failed to create RAM file %s\n", treefile);


warning: do not call c-style vararg functions [cppcoreguidelines-pro-type-vararg]

printf("Failed to create RAM file %s\n", treefile); ^

github-actions · 2025-11-16T07:57:51Z

src/ramcore/SamToNTuple.cxx

    ramcore::SamParser parser;
-
+
+    int64_t mapped_count = 0;


warning: no header providing "int64_t" is directly included [misc-include-cleaner]

int64_t mapped_count = 0; ^

github-actions · 2025-11-16T07:57:51Z

src/ramcore/SamToNTuple.cxx

-
+
+    int64_t mapped_count = 0;
+    int32_t last_refid = -2;


warning: no header providing "int32_t" is directly included [misc-include-cleaner]

int32_t last_refid = -2; ^

github-actions · 2025-11-16T07:57:51Z

test/ramcoretests.cxx

 #include <filesystem>
-#include <Rtypes.h>
+#include <regex>
+#include "../tools/ramview.cxx"


warning: included header regex is not used directly [misc-include-cleaner]

Suggested change

#include "../tools/ramview.cxx"

#include "../tools/ramview.cxx"

github-actions · 2025-11-16T07:57:52Z

test/ramcoretests.cxx

 #include <filesystem>
-#include <Rtypes.h>
+#include <regex>
+#include "../tools/ramview.cxx"


warning: suspicious #include of file with '.cxx' extension [bugprone-suspicious-include]

#include "../tools/ramview.cxx" ^

github-actions · 2025-11-16T07:57:52Z

test/ramcoretests.cxx


-      testing::internal::GetCapturedStdout();
+    testing::internal::CaptureStdout();
+    ramview(ttreeFile, region, true, false, nullptr);


warning: argument comment missing for literal argument 'cache' [bugprone-argument-comment]

Suggested change

ramview(ttreeFile, region, true, false, nullptr);

ramview(ttreeFile, region, /*cache=*/true, false, nullptr);

github-actions · 2025-11-16T07:57:52Z

test/ramcoretests.cxx


-      testing::internal::GetCapturedStdout();
+    testing::internal::CaptureStdout();
+    ramview(ttreeFile, region, true, false, nullptr);


warning: argument comment missing for literal argument 'perfstats' [bugprone-argument-comment]

Suggested change

ramview(ttreeFile, region, true, false, nullptr);

ramview(ttreeFile, region, true, /*perfstats=*/false, nullptr);

codecov-commenter · 2025-11-16T08:00:37Z

Codecov Report

❌ Patch coverage is 42.53247% with 177 lines in your changes missing coverage. Please review.
⚠️ Please upload report for BASE (develop@9028ee7). Learn more about missing BASE report.

Files with missing lines	Patch %	Lines
src/ramcore/RAMNTupleView.cxx	25.80%	60 Missing and 9 partials ⚠️
tools/samtoramntuple.cxx	0.00%	51 Missing ⚠️
src/rntuple/RAMNTupleRecord.cxx	0.00%	22 Missing ⚠️
src/ramcore/SamToNTuple.cxx	83.75%	6 Missing and 7 partials ⚠️
tools/ramview.cxx	58.62%	6 Missing and 6 partials ⚠️
test/ramcoretests.cxx	69.69%	1 Missing and 9 partials ⚠️

❌ Your patch status has failed because the patch coverage (42.53%) is below the target coverage (85.00%). You can increase the patch coverage or adjust the target coverage.

Additional details and impacted files

@@            Coverage Diff             @@
##             develop      #13   +/-   ##
==========================================
  Coverage           ?   53.02%           
==========================================
  Files              ?       16           
  Lines              ?     1439           
  Branches           ?      739           
==========================================
  Hits               ?      763           
  Misses             ?      552           
  Partials           ?      124

Flag	Coverage Δ
unittests	`53.02% <42.53%> (?)`

Flags with carried forward coverage won't be shown. Click here to find out more.

Files with missing lines	Coverage Δ
test/ramcoretests.cxx	`69.69% <69.69%> (ø)`
tools/ramview.cxx	`56.41% <58.62%> (ø)`
src/ramcore/SamToNTuple.cxx	`89.65% <83.75%> (ø)`
src/rntuple/RAMNTupleRecord.cxx	`35.49% <0.00%> (ø)`
tools/samtoramntuple.cxx	`0.00% <0.00%> (ø)`
src/ramcore/RAMNTupleView.cxx	`29.82% <25.80%> (ø)`

Files with missing lines	Coverage Δ
test/ramcoretests.cxx	`69.69% <69.69%> (ø)`
tools/ramview.cxx	`56.41% <58.62%> (ø)`
src/ramcore/SamToNTuple.cxx	`89.65% <83.75%> (ø)`
src/rntuple/RAMNTupleRecord.cxx	`35.49% <0.00%> (ø)`
tools/samtoramntuple.cxx	`0.00% <0.00%> (ø)`
src/ramcore/RAMNTupleView.cxx	`29.82% <25.80%> (ø)`

🚀 New features to boost your workflow:

❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

github-actions

clang-tidy made some suggestions

github-actions · 2025-11-16T10:53:43Z

src/ramcore/RAMNTupleView.cxx

 #include <cstring>
+#include <iostream>
+#include <limits>
+#include <string>


warning: included header limits is not used directly [misc-include-cleaner]

Suggested change

#include <string>

#include <string>

github-actions · 2025-11-16T10:53:43Z

src/ramcore/SamToNTuple.cxx

 #include <TFile.h>
 #include <TROOT.h>

+#include <cstdint>


warning: #includes are not sorted properly [llvm-include-order]

#include <cstdint> ^

this fix will not be applied because it overlaps with another fix

github-actions · 2025-11-16T10:53:43Z

test/ramcoretests.cxx


-      testing::internal::GetCapturedStdout();
+    testing::internal::CaptureStdout();
+    ramview(ttreeFile, region, /*cache=*/true, /*perfstats=*/false, nullptr);


warning: argument comment missing for literal argument 'perfstatsfilename' [bugprone-argument-comment]

Suggested change

ramview(ttreeFile, region, /*cache=*/true, /*perfstats=*/false, nullptr);

ramview(ttreeFile, region, /*cache=*/true, /*perfstats=*/false, /*perfstatsfilename=*/nullptr);

github-actions · 2025-11-16T10:53:43Z

test/ramcoretests.cxx

-      testing::internal::GetCapturedStdout();
+    testing::internal::CaptureStdout();
+    ramview(ttreeFile, region, /*cache=*/true, /*perfstats=*/false, nullptr);
+    std::string ramview_output = testing::internal::GetCapturedStdout();


warning: no header providing "std::string" is directly included [misc-include-cleaner]

test/ramcoretests.cxx:11:

+ #include <string>

github-actions · 2025-11-16T10:53:43Z

test/ramcoretests.cxx

-      testing::internal::GetCapturedStdout();
+    testing::internal::CaptureStdout();
+    ramview(ttreeFile, region, /*cache=*/true, /*perfstats=*/false, nullptr);
+    std::string ramview_output = testing::internal::GetCapturedStdout();


warning: variable 'ramview_output' is not initialized [cppcoreguidelines-init-variables]

Suggested change

std::string ramview_output = testing::internal::GetCapturedStdout();

std::string ramview_output = 0 = testing::internal::GetCapturedStdout();

github-actions · 2025-11-16T10:53:44Z

test/ramcoretests.cxx

-   }
+    testing::internal::CaptureStdout();
+    ramntupleview(rntupleFile, region, /*cache=*/true, /*perfstats=*/false, nullptr);
+    std::string ramntupleview_output = testing::internal::GetCapturedStdout();


warning: variable 'ramntupleview_output' is not initialized [cppcoreguidelines-init-variables]

Suggested change

std::string ramntupleview_output = testing::internal::GetCapturedStdout();

std::string ramntupleview_output = 0 = testing::internal::GetCapturedStdout();

github-actions · 2025-11-16T10:53:44Z

tools/samtoramntuple.cxx

 #include <string>
 #include <cstring>
+#include <vector>



warning: included header vector is not used directly [misc-include-cleaner]

Suggested change

github-actions · 2025-11-16T10:53:44Z

tools/samtoramntuple.cxx

           do_split = true;
+        } else if (arg == "-only") {
+           if (i + 1 < argc) {
+              only_chromosomes.emplace_back(argv[++i]);


warning: do not use pointer arithmetic [cppcoreguidelines-pro-bounds-pointer-arithmetic]

only_chromosomes.emplace_back(argv[++i]); ^

github-actions

clang-tidy made some suggestions

There were too many comments to post at once. Showing the first 10 out of 23. Check the log or trigger a new build to see more.

github-actions · 2025-11-16T12:44:22Z

src/ramcore/SamToNTuple.cxx

 #include "ramcore/SamParser.h"
 #include "rntuple/RAMNTupleRecord.h"

+#include <cstdint>


warning: #includes are not sorted properly [llvm-include-order]

#include <cstdint> ^

this fix will not be applied because it overlaps with another fix

github-actions · 2025-11-16T12:44:23Z

src/ramcore/SamToNTuple.cxx


+#include <cstdint>
+#include <map>
+#include <memory>


warning: included header map is not used directly [misc-include-cleaner]

Suggested change

#include <memory>

#include <memory>

github-actions · 2025-11-16T12:44:23Z

src/ramcore/SamToNTuple.cxx

+#include <cstdint>
+#include <map>
+#include <memory>
+#include <cstdio>


warning: included header memory is not used directly [misc-include-cleaner]

Suggested change

#include <cstdio>

#include <cstdio>

github-actions · 2025-11-16T12:44:23Z

src/ramcore/SamToNTuple.cxx

+#include <memory>
+#include <cstdio>
+#include <thread>
+#include <vector>


warning: included header thread is not used directly [misc-include-cleaner]

Suggested change

#include <vector>

#include <vector>

github-actions · 2025-11-16T12:44:23Z

src/ramcore/SamToNTuple.cxx

+#include <cstdio>
+#include <thread>
+#include <vector>
+#include <mutex>


warning: included header vector is not used directly [misc-include-cleaner]

Suggested change

#include <mutex>

#include <mutex>

github-actions · 2025-11-16T12:44:23Z

src/ramcore/SamToNTuple.cxx

+#include <mutex>
+#include <algorithm>
+#include <unordered_set>
+


warning: included header unordered_set is not used directly [misc-include-cleaner]

Suggested change

github-actions · 2025-11-16T12:44:23Z

src/ramcore/SamToNTuple.cxx

-                    bool index, bool split, bool cache,
-                    int compression_algorithm,
-                    uint32_t quality_policy)
+void samtoramntuple(const char *datafile, const char *treefile, bool index, bool split, bool cache,


warning: function 'samtoramntuple' can be made static or moved into an anonymous namespace to enforce internal linkage [misc-use-internal-linkage]

Suggested change

void samtoramntuple(const char *datafile, const char *treefile, bool index, bool split, bool cache,

static void samtoramntuple(const char *datafile, const char *treefile, bool index, bool split, bool cache,

github-actions · 2025-11-16T12:44:23Z

src/ramcore/SamToNTuple.cxx

+   const int32_t POS_INTERVAL = 10000;
+   const int64_t MAPPED_INTERVAL = 100;
+
+   auto header_callback = [&headers](const std::string &tag, const std::string &content) {


warning: no header providing "std::string" is directly included [misc-include-cleaner]

src/ramcore/SamToNTuple.cxx:9:

- #include <vector> + #include <string> + #include <vector>

github-actions · 2025-11-16T12:44:23Z

src/ramcore/SamToNTuple.cxx

+         if (sn_pos != std::string::npos) {
+            sn_pos += 3;
+            size_t tab_pos = content.find('\t', sn_pos);
+            std::string ref_name =


warning: variable 'ref_name' is not initialized [cppcoreguidelines-init-variables]

Suggested change

std::string ref_name =

std::string ref_name = 0 =

github-actions · 2025-11-16T12:44:23Z

src/ramcore/SamToNTuple.cxx

+   };
+
+   if (!parser.ParseFile(datafile, header_callback, record_callback)) {
+      printf("Failed to parse SAM file %s\n", datafile);


warning: do not call c-style vararg functions [cppcoreguidelines-pro-type-vararg]

printf("Failed to parse SAM file %s\n", datafile); ^

github-actions

clang-tidy made some suggestions

There were too many comments to post at once. Showing the first 10 out of 18. Check the log or trigger a new build to see more.

github-actions · 2025-11-16T14:28:18Z

src/ramcore/SamToNTuple.cxx

+#include <cstdio>
+#include <map>
+#include <memory>
+#include <mutex>


warning: included header memory is not used directly [misc-include-cleaner]

Suggested change

#include <mutex>

#include <mutex>

github-actions · 2025-11-16T14:28:19Z

src/ramcore/SamToNTuple.cxx

+#include <mutex>
+#include <string>
+#include <thread>
+#include <unordered_set>


warning: included header thread is not used directly [misc-include-cleaner]

Suggested change

#include <unordered_set>

#include <unordered_set>

github-actions · 2025-11-16T14:28:19Z

src/ramcore/SamToNTuple.cxx

+#include <string>
+#include <thread>
+#include <unordered_set>
+#include <vector>


warning: included header unordered_set is not used directly [misc-include-cleaner]

Suggested change

#include <vector>

#include <vector>

github-actions · 2025-11-16T14:28:19Z

src/ramcore/SamToNTuple.cxx

+#include <thread>
+#include <unordered_set>
+#include <vector>
+


warning: included header vector is not used directly [misc-include-cleaner]

Suggested change

github-actions · 2025-11-16T14:28:19Z

src/ramcore/SamToNTuple.cxx

-                    bool index, bool split, bool cache,
-                    int compression_algorithm,
-                    uint32_t quality_policy)
+void samtoramntuple(const char *datafile, const char *treefile, bool index, bool split,


warning: function 'samtoramntuple' can be made static or moved into an anonymous namespace to enforce internal linkage [misc-use-internal-linkage]

Suggested change

void samtoramntuple(const char *datafile, const char *treefile, bool index, bool split,

static void samtoramntuple(const char *datafile, const char *treefile, bool index, bool split,

github-actions · 2025-11-16T14:28:19Z

test/ramcoretests.cxx

-        if (!std::filesystem::exists("samexample.sam")) {
-            GenerateSAMFile("samexample.sam", num_reads_for_test);
-        }
+   void SetUp() override


warning: method 'SetUp' can be made static [readability-convert-member-functions-to-static]

Suggested change

void SetUp() override

static void SetUp() override

github-actions · 2025-11-16T14:28:19Z

test/ramcoretests.cxx

-        std::remove("test_ttree.root");
-        std::remove("test_rntuple.root");
-    }
+   void TearDown() override


warning: method 'TearDown' can be made static [readability-convert-member-functions-to-static]

Suggested change

void TearDown() override

static void TearDown() override

github-actions · 2025-11-16T14:28:19Z

test/ramcoretests.cxx

-}
-
-TEST_F(ramcoreTest, RNTupleView)
+TEST_F(ramcoreTest, ConversionProducesEqualEntries)


warning: function 'TEST_F' can be made static or moved into an anonymous namespace to enforce internal linkage [misc-use-internal-linkage]

Suggested change

TEST_F(ramcoreTest, ConversionProducesEqualEntries)

TEST_Fstatic (ramcoreTest, ConversionProducesEqualEntries)

github-actions · 2025-11-16T14:28:19Z

test/ramcoretests.cxx

-   }
+   testing::internal::CaptureStdout();
+   ramview(ttreeFile, region, /*cache=*/true, /*perfstats=*/false, /*perfstatsfilename=*/nullptr);
+   std::string ramview_output;


warning: variable 'ramview_output' is not initialized [cppcoreguidelines-init-variables]

Suggested change

std::string ramview_output;

std::string ramview_output = 0;

github-actions · 2025-11-16T14:28:19Z

test/ramcoretests.cxx

-   ASSERT_NE(reader, nullptr) << "RNTuple file corrupted after viewing";
+   testing::internal::CaptureStdout();
+   ramntupleview(rntupleFile, region, /*cache=*/true, /*perfstats=*/false, /*perfstatsfilename=*/nullptr);
+   std::string ramntupleview_output;


warning: variable 'ramntupleview_output' is not initialized [cppcoreguidelines-init-variables]

Suggested change

std::string ramntupleview_output;

std::string ramntupleview_output = 0;

github-actions

clang-tidy made some suggestions

github-actions · 2025-11-16T14:39:19Z

tools/samtoramntuple.cxx

+int main(int argc, char *argv[])
+{
+   if (argc < 2) {
+      std::cout << "Usage: " << argv[0] << " <input.sam> [output]\n";


warning: do not use pointer arithmetic [cppcoreguidelines-pro-bounds-pointer-arithmetic]

std::cout << "Usage: " << argv[0] << " <input.sam> [output]\n"; ^

github-actions · 2025-11-16T14:39:19Z

tools/samtoramntuple.cxx

-           output = argv[i];
-        }
-    }
+   const char *input = argv[1];


warning: do not use pointer arithmetic [cppcoreguidelines-pro-bounds-pointer-arithmetic]

const char *input = argv[1]; ^

github-actions · 2025-11-16T14:39:19Z

tools/samtoramntuple.cxx

-    return 0;
-}
+   for (int i = 2; i < argc; i++) {
+      std::string arg = argv[i];


warning: do not use pointer arithmetic [cppcoreguidelines-pro-bounds-pointer-arithmetic]

std::string arg = argv[i]; ^

github-actions · 2025-11-16T14:39:19Z

tools/samtoramntuple.cxx

+      } else if (arg == "-only") {
+         if (i + 1 < argc) {
+
+            only_chromosomes.emplace_back(argv[++i]);


warning: do not use pointer arithmetic [cppcoreguidelines-pro-bounds-pointer-arithmetic]

only_chromosomes.emplace_back(argv[++i]); ^

github-actions · 2025-11-16T14:39:19Z

tools/samtoramntuple.cxx

+         }
+      } else if (arg == "-noindex") {
+         do_index = false;
+      } else if (arg == "-illumina") {


warning: repeated branch body in conditional chain [bugprone-branch-clone]

} else if (arg == "-illumina") { ^

Additional context

tools/samtoramntuple.cxx:44: end of the original

} else if (arg == "-dropqual") { ^

tools/samtoramntuple.cxx:44: clone 1 starts here

} else if (arg == "-dropqual") { ^

github-actions · 2025-11-16T14:39:19Z

tools/samtoramntuple.cxx

+      } else if (arg == "-dropqual") {
+         quality_mode = RAMNTupleRecord::kDrop;
+      } else if (arg[0] != '-') {
+         output = argv[i];


warning: do not use pointer arithmetic [cppcoreguidelines-pro-bounds-pointer-arithmetic]

output = argv[i]; ^

github-actions · 2025-11-16T14:39:19Z

tools/samtoramntuple.cxx

+      }
+   }
+
+   std::string outfile;


warning: variable 'outfile' is not initialized [cppcoreguidelines-init-variables]

Suggested change

std::string outfile;

std::string outfile = 0;

github-actions · 2025-11-16T14:39:19Z

tools/samtoramntuple.cxx

+         }
+         samtoramntuple(input, ramfile.c_str(), do_index, true, true, 505, quality_mode);
+      }
+   } catch (const std::exception &e) {


warning: no header providing "std::exception" is directly included [misc-include-cleaner]

tools/samtoramntuple.cxx:2:

- #include <iostream> + #include <exception> + #include <iostream>

github-actions

clang-tidy made some suggestions

github-actions · 2025-12-03T16:18:15Z

src/ramcore/SamToNTuple.cxx

+#include <cstdint>
+#include <cstdio>
+#include <map>
+#include <memory> // NOLINT(misc-include-cleaner) - used for std::unique_ptr


warning: included header map is not used directly [misc-include-cleaner]

Suggested change

#include <memory> // NOLINT(misc-include-cleaner) - used for std::unique_ptr

#include <memory> // NOLINT(misc-include-cleaner) - used for std::unique_ptr

github-actions · 2025-12-03T16:18:15Z

src/ramcore/SamToNTuple.cxx

-                    bool index, bool split, bool cache,
-                    int compression_algorithm,
-                    uint32_t quality_policy)
+void samtoramntuple(const char *datafile, const char *treefile, bool index,


warning: function 'samtoramntuple' can be made static or moved into an anonymous namespace to enforce internal linkage [misc-use-internal-linkage]

Suggested change

void samtoramntuple(const char *datafile, const char *treefile, bool index,

static void samtoramntuple(const char *datafile, const char *treefile, bool index,

github-actions · 2025-12-03T16:18:16Z

test/ramcoretests.cxx

-   }
+   testing::internal::CaptureStdout();
+   ramview(ttreeFile, region, /*cache=*/true, /*perfstats=*/false, /*perfstatsfilename=*/nullptr);
+   std::string ramview_output = testing::internal::GetCapturedStdout();


warning: variable 'ramview_output' is not initialized [cppcoreguidelines-init-variables]

Suggested change

std::string ramview_output = testing::internal::GetCapturedStdout();

std::string ramview_output = 0 = testing::internal::GetCapturedStdout();

github-actions · 2025-12-03T16:18:16Z

test/ramcoretests.cxx

-   ASSERT_NE(reader, nullptr) << "RNTuple file corrupted after viewing";
+   testing::internal::CaptureStdout();
+   ramntupleview(rntupleFile, region, /*cache=*/true, /*perfstats=*/false, /*perfstatsfilename=*/nullptr);
+   std::string ramntupleview_output = testing::internal::GetCapturedStdout();


warning: variable 'ramntupleview_output' is not initialized [cppcoreguidelines-init-variables]

Suggested change

std::string ramntupleview_output = testing::internal::GetCapturedStdout();

std::string ramntupleview_output = 0 = testing::internal::GetCapturedStdout();

github-actions · 2025-12-03T16:18:16Z

tools/samtoramntuple.cxx

@@ -1,67 +1,80 @@
 #include "ramcore/SamToNTuple.h"


warning: 'ramcore/SamToNTuple.h' file not found [clang-diagnostic-error]

#include "ramcore/SamToNTuple.h" ^

github-actions · 2025-12-03T16:18:16Z

tools/samtoramntuple.cxx

+#include <exception>
 #include <iostream>
 #include <string>
 #include <cstring>


warning: #includes are not sorted properly [llvm-include-order]

Suggested change

#include <cstring>

#include <cstring>

#include <exception>

#include <iostream>

#include <string>

github-actions · 2025-12-03T16:18:16Z

tools/samtoramntuple.cxx

+int main(int argc, char *argv[])
+{
+   if (argc < 2) {
+      std::cout << "Usage: " << argv[0]


warning: do not use pointer arithmetic [cppcoreguidelines-pro-bounds-pointer-arithmetic]

std::cout << "Usage: " << argv[0] ^

github-actions · 2025-12-03T16:18:16Z

tools/samtoramntuple.cxx

+         }
+      } else if (arg == "-noindex") {
+         do_index = false;
+      } else if (arg == "-illumina") {


warning: repeated branch body in conditional chain [bugprone-branch-clone]

} else if (arg == "-illumina") { ^

github-actions

clang-tidy made some suggestions

github-actions · 2025-12-04T13:25:22Z

src/ramcore/SamToNTuple.cxx

-void samtoramntuple(const char *datafile,
-                    const char *treefile,
-                    bool index, bool split, bool cache,
+void samtoramntuple(const char *datafile, const char *treefile, bool index, bool split, bool cache,


warning: function 'samtoramntuple' can be made static or moved into an anonymous namespace to enforce internal linkage [misc-use-internal-linkage]

Suggested change

void samtoramntuple(const char *datafile, const char *treefile, bool index, bool split, bool cache,

static void samtoramntuple(const char *datafile, const char *treefile, bool index, bool split, bool cache,

github-actions · 2025-12-04T13:25:22Z

test/ramcoretests.cxx

-    ASSERT_TRUE(ft && !ft->IsZombie()) << "Failed to open TTree file";
+class ramcoreTest : public ::testing::Test {
+protected:
+   const int m_num_reads_for_test = 100;


warning: member 'm_num_reads_for_test' of type 'const int' is const qualified [cppcoreguidelines-avoid-const-or-ref-data-members]

const int m_num_reads_for_test = 100; ^

github-actions · 2025-12-04T13:25:23Z

test/ramcoretests.cxx

-    ASSERT_TRUE(ft && !ft->IsZombie()) << "Failed to open TTree file";
+class ramcoreTest : public ::testing::Test {
+protected:
+   const int m_num_reads_for_test = 100;


warning: member variable 'm_num_reads_for_test' has protected visibility [cppcoreguidelines-non-private-member-variables-in-classes]

const int m_num_reads_for_test = 100; ^

github-actions · 2025-12-04T13:25:23Z

test/ramcoretests.cxx

+class ramcoreTest : public ::testing::Test {
+protected:
+   const int m_num_reads_for_test = 100;
+   const std::string m_samFile = "samexample.sam";


warning: member 'm_samFile' of type 'const std::string' (aka 'const int') is const qualified [cppcoreguidelines-avoid-const-or-ref-data-members]

const std::string m_samFile = "samexample.sam"; ^

github-actions · 2025-12-04T13:25:23Z

test/ramcoretests.cxx

+class ramcoreTest : public ::testing::Test {
+protected:
+   const int m_num_reads_for_test = 100;
+   const std::string m_samFile = "samexample.sam";


warning: member variable 'm_samFile' has public visibility [cppcoreguidelines-non-private-member-variables-in-classes]

const std::string m_samFile = "samexample.sam"; ^

github-actions · 2025-12-04T13:25:23Z

test/ramcoretests.cxx

+protected:
+   const int m_num_reads_for_test = 100;
+   const std::string m_samFile = "samexample.sam";
+   const std::string m_ttreeFile = "test_ttree.root";


warning: member 'm_ttreeFile' of type 'const std::string' (aka 'const int') is const qualified [cppcoreguidelines-avoid-const-or-ref-data-members]

const std::string m_ttreeFile = "test_ttree.root"; ^

github-actions · 2025-12-04T13:25:23Z

test/ramcoretests.cxx

+protected:
+   const int m_num_reads_for_test = 100;
+   const std::string m_samFile = "samexample.sam";
+   const std::string m_ttreeFile = "test_ttree.root";


warning: member variable 'm_ttreeFile' has public visibility [cppcoreguidelines-non-private-member-variables-in-classes]

const std::string m_ttreeFile = "test_ttree.root"; ^

github-actions · 2025-12-04T13:25:23Z

test/ramcoretests.cxx

+   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";


warning: member 'm_rntupleFile' of type 'const std::string' (aka 'const int') is const qualified [cppcoreguidelines-avoid-const-or-ref-data-members]

const std::string m_rntupleFile = "test_rntuple.root"; ^

github-actions · 2025-12-04T13:25:23Z

test/ramcoretests.cxx

+   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";


warning: member variable 'm_rntupleFile' has public visibility [cppcoreguidelines-non-private-member-variables-in-classes]

const std::string m_rntupleFile = "test_rntuple.root"; ^

Signed-off-by: AdityaPandeyCN <[email protected]> clang changes Signed-off-by: AdityaPandeyCN <[email protected]>

Signed-off-by: AdityaPandeyCN <[email protected]>

github-actions

clang-tidy made some suggestions

github-actions · 2025-12-04T13:41:35Z

test/ramcoretests.cxx

-    samtoram(samFile, ttreeFile, true, true, true, 1, 0);
-    samtoramntuple(samFile, rntupleFile, true, true, true, 505, 0);
+constexpr int kNumReadsForTest = 100;
+constexpr const char kSamFile[] = "samexample.sam";


warning: do not declare C-style arrays, use std::array<> instead [cppcoreguidelines-avoid-c-arrays]

constexpr const char kSamFile[] = "samexample.sam"; ^

github-actions · 2025-12-04T13:41:36Z

test/ramcoretests.cxx

-    samtoramntuple(samFile, rntupleFile, true, true, true, 505, 0);
+constexpr int kNumReadsForTest = 100;
+constexpr const char kSamFile[] = "samexample.sam";
+constexpr const char kTTreeFile[] = "test_ttree.root";


warning: do not declare C-style arrays, use std::array<> instead [cppcoreguidelines-avoid-c-arrays]

constexpr const char kTTreeFile[] = "test_ttree.root"; ^

github-actions · 2025-12-04T13:41:36Z

test/ramcoretests.cxx

+constexpr int kNumReadsForTest = 100;
+constexpr const char kSamFile[] = "samexample.sam";
+constexpr const char kTTreeFile[] = "test_ttree.root";
+constexpr const char kRNTupleFile[] = "test_rntuple.root";


warning: do not declare C-style arrays, use std::array<> instead [cppcoreguidelines-avoid-c-arrays]

constexpr const char kRNTupleFile[] = "test_rntuple.root"; ^

github-actions · 2025-12-04T13:41:36Z

test/ramcoretests.cxx

-    auto reader = ROOT::RNTupleReader::Open("RAM", rntupleFile);
-    ASSERT_NE(reader, nullptr) << "Failed to open RNTuple";
-    Long64_t rntupleEntries = reader->GetNEntries();
+      std::remove(kTTreeFile);


warning: do not implicitly decay an array into a pointer; consider using gsl::array_view or an explicit cast instead [cppcoreguidelines-pro-bounds-array-to-pointer-decay]

std::remove(kTTreeFile); ^

github-actions · 2025-12-04T13:41:36Z

test/ramcoretests.cxx

-    ASSERT_NE(reader, nullptr) << "Failed to open RNTuple";
-    Long64_t rntupleEntries = reader->GetNEntries();
+      std::remove(kTTreeFile);
+      std::remove(kRNTupleFile);


warning: do not implicitly decay an array into a pointer; consider using gsl::array_view or an explicit cast instead [cppcoreguidelines-pro-bounds-array-to-pointer-decay]

std::remove(kRNTupleFile); ^

github-actions · 2025-12-04T13:41:36Z

test/ramcoretests.cxx

-}
+   void TearDown() override
+   {
+      std::remove(kTTreeFile);


warning: do not implicitly decay an array into a pointer; consider using gsl::array_view or an explicit cast instead [cppcoreguidelines-pro-bounds-array-to-pointer-decay]

std::remove(kTTreeFile); ^

github-actions · 2025-12-04T13:41:36Z

test/ramcoretests.cxx

+   void TearDown() override
+   {
+      std::remove(kTTreeFile);
+      std::remove(kRNTupleFile);


warning: do not implicitly decay an array into a pointer; consider using gsl::array_view or an explicit cast instead [cppcoreguidelines-pro-bounds-array-to-pointer-decay]

std::remove(kRNTupleFile); ^

github-actions · 2025-12-04T13:41:36Z

test/ramcoretests.cxx


-      testing::internal::GetCapturedStdout();
+   testing::internal::CaptureStdout();
+   ramview(kTTreeFile, region, /*cache=*/true, /*perfstats=*/false, /*perfstatsfilename=*/nullptr);


warning: do not implicitly decay an array into a pointer; consider using gsl::array_view or an explicit cast instead [cppcoreguidelines-pro-bounds-array-to-pointer-decay]

ramview(kTTreeFile, region, /*cache=*/true, /*perfstats=*/false, /*perfstatsfilename=*/nullptr); ^

Signed-off-by: AdityaPandeyCN <[email protected]>

github-actions

clang-tidy made some suggestions

github-actions · 2025-12-04T13:55:54Z

test/ramcoretests.cxx

-#include <Rtypes.h>
+#include <string>
+#include <string_view>



warning: included header string_view is not used directly [misc-include-cleaner]

Suggested change

Signed-off-by: AdityaPandeyCN <[email protected]>

mvassilev · 2025-12-05T15:11:42Z

LGTM!

AdityaPandeyCN marked this pull request as draft November 16, 2025 06:26

github-actions bot reviewed Nov 16, 2025

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AdityaPandeyCN force-pushed the index_scan branch from a89b30d to bcde36d Compare November 16, 2025 14:28

AdityaPandeyCN marked this pull request as ready for review November 16, 2025 14:33

github-actions bot reviewed Nov 16, 2025

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github-actions bot reviewed Dec 3, 2025

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github-actions bot reviewed Dec 4, 2025

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AdityaPandeyCN added 2 commits December 4, 2025 18:57

repairing indexing of root file

fb2a682

Signed-off-by: AdityaPandeyCN <[email protected]> clang changes Signed-off-by: AdityaPandeyCN <[email protected]>

clang changes

f737701

Signed-off-by: AdityaPandeyCN <[email protected]>

AdityaPandeyCN force-pushed the index_scan branch from f6e9e94 to f737701 Compare December 4, 2025 13:33

github-actions bot reviewed Dec 4, 2025

View reviewed changes

clang changes

f9870c5

Signed-off-by: AdityaPandeyCN <[email protected]>

github-actions bot reviewed Dec 4, 2025

View reviewed changes

AdityaPandeyCN added 2 commits December 4, 2025 19:30

clang changes

9fb2942

Signed-off-by: AdityaPandeyCN <[email protected]>

clang changes

f549654

Signed-off-by: AdityaPandeyCN <[email protected]>

	const std::vector<std::string> RegionQueryFixture::regions_ = {"1:1000000-1001000",
	const std::vector<std::string> RegionQueryFixture::regions = {"1:1000000-1001000",

	BENCHMARK_REGISTER_F(RegionQueryFixture, TTree)->DenseRange(0, 17, 1)->Unit(benchmark::kSecond);
	BENCHMARK_REGISTER_Fstatic (RegionQueryFixture, TTree)->DenseRange(0, 17, 1)->Unit(benchmark::kSecond);

	const std::vector<std::string> &only_chromosomes = {});
	std::vector<std::string> &only_chromosomes = {});

		@@ -1,6 +1,9 @@
		#include "ramcore/RAMNTupleView.h"
		#include <cstdint>


		stopwatch.Print();

		printf("Found %lld records in region %s\n", static_cast<long long>(count), query ? query : "");

	#include "../tools/ramview.cxx"
	#include "../tools/ramview.cxx"

	ramview(ttreeFile, region, true, false, nullptr);
	ramview(ttreeFile, region, /cache=/true, false, nullptr);

	ramview(ttreeFile, region, true, false, nullptr);
	ramview(ttreeFile, region, true, /perfstats=/false, nullptr);

	std::string ramview_output = testing::internal::GetCapturedStdout();
	std::string ramview_output = 0 = testing::internal::GetCapturedStdout();

	std::string ramntupleview_output = testing::internal::GetCapturedStdout();
	std::string ramntupleview_output = 0 = testing::internal::GetCapturedStdout();

	void samtoramntuple(const char datafile, const char treefile, bool index, bool split, bool cache,
	static void samtoramntuple(const char datafile, const char treefile, bool index, bool split, bool cache,

	TEST_F(ramcoreTest, ConversionProducesEqualEntries)
	TEST_Fstatic (ramcoreTest, ConversionProducesEqualEntries)

	std::string ramntupleview_output;
	std::string ramntupleview_output = 0;

	#include <memory> // NOLINT(misc-include-cleaner) - used for std::unique_ptr
	#include <memory> // NOLINT(misc-include-cleaner) - used for std::unique_ptr

Index Repairing of RNTuple ROOT file #13

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AdityaPandeyCN commented Nov 16, 2025 •

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