Index Repairing of RNTuple ROOT file #13
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Signed-off-by: AdityaPandeyCN <adityapand3y666@gmail.com>
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| @@ -1,6 +1,6 @@ | |||
| #include <benchmark/benchmark.h> | |||
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warning: 'benchmark/benchmark.h' file not found [clang-diagnostic-error]
#include <benchmark/benchmark.h>
^| "chr21:1-48129895", | ||
| "chrM:1-16571", | ||
| "chrY:2600000-2700000", | ||
| const std::vector<std::string> RegionQueryFixture::regions_ = {"1:1000000-1001000", |
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warning: invalid case style for variable 'regions_' [readability-identifier-naming]
| 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)->Args({0})->Args({3})->Args({6})->Args({9})->Unit(benchmark::kSecond); | ||
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| 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); |
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warning: function 'BENCHMARK_REGISTER_F' can be made static or moved into an anonymous namespace to enforce internal linkage [misc-use-internal-linkage]
| BENCHMARK_REGISTER_F(RegionQueryFixture, TTree)->DenseRange(0, 17, 1)->Unit(benchmark::kSecond); | |
| BENCHMARK_REGISTER_Fstatic (RegionQueryFixture, TTree)->DenseRange(0, 17, 1)->Unit(benchmark::kSecond); |
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| 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); |
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warning: function 'BENCHMARK_REGISTER_F' can be made static or moved into an anonymous namespace to enforce internal linkage [misc-use-internal-linkage]
| BENCHMARK_REGISTER_F(RegionQueryFixture, RNTuple)->DenseRange(0, 17, 1)->Unit(benchmark::kSecond); | |
| BENCHMARK_REGISTER_Fstatic (RegionQueryFixture, RNTuple)->DenseRange(0, 17, 1)->Unit(benchmark::kSecond); |
| #ifndef RAMCORE_SAMTONTUPLE_H | ||
| #define RAMCORE_SAMTONTUPLE_H | ||
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| #include <cstdint> |
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warning: 'cstdint' file not found [clang-diagnostic-error]
#include <cstdint>
^| 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 = {}); |
There was a problem hiding this comment.
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]
| const std::vector<std::string> &only_chromosomes = {}); | |
| std::vector<std::string> &only_chromosomes = {}); |
| @@ -1,6 +1,7 @@ | |||
| #include "ramcore/RAMNTupleView.h" | |||
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warning: 'ramcore/RAMNTupleView.h' file not found [clang-diagnostic-error]
#include "ramcore/RAMNTupleView.h"
^| #include <iostream> | ||
| #include <cstring> | ||
| #include <limits> | ||
| #include <ROOT/RNTuple.hxx> |
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warning: included header limits is not used directly [misc-include-cleaner]
| #include <ROOT/RNTuple.hxx> | |
| #include <ROOT/RNTuple.hxx> |
| int rangeDelimiterPos = region.find("-", chrDelimiterPos); | ||
| if (rangeDelimiterPos == std::string::npos) { | ||
| try { | ||
| range_start = std::stoi(region.substr(chrDelimiterPos + 1)); |
There was a problem hiding this comment.
warning: no header providing "std::stoi" is directly included [misc-include-cleaner]
range_start = std::stoi(region.substr(chrDelimiterPos + 1));
^|
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| auto recordView = reader->GetView<RAMNTupleRecord>("record"); | ||
| auto flagView = reader->GetView<uint16_t>("record.flag"); | ||
| auto refidView = reader->GetView<int32_t>("record.refid"); |
There was a problem hiding this comment.
warning: no header providing "int32_t" is directly included [misc-include-cleaner]
src/ramcore/RAMNTupleView.cxx:1:
- #include <iostream>
+ #include <cstdint>
+ #include <iostream>
| @@ -1,6 +1,9 @@ | |||
| #include "ramcore/RAMNTupleView.h" | |||
| #include <cstdint> | |||
There was a problem hiding this comment.
warning: #includes are not sorted properly [llvm-include-order]
#include <cstdint>
^this fix will not be applied because it overlaps with another fix
src/ramcore/RAMNTupleView.cxx
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| stopwatch.Print(); | ||
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| printf("Found %lld records in region %s\n", static_cast<long long>(count), query ? query : ""); |
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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 : "");
^
src/ramcore/SamToNTuple.cxx
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| #include <mutex> | ||
| #include <algorithm> | ||
| #include <unordered_set> | ||
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warning: included header unordered_set is not used directly [misc-include-cleaner]
src/ramcore/SamToNTuple.cxx
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| auto rootFile = std::unique_ptr<TFile>(TFile::Open(treefile, "RECREATE")); | ||
| if (!rootFile || !rootFile->IsOpen()) { | ||
| printf("Failed to create RAM file %s\n", treefile); |
There was a problem hiding this comment.
warning: do not call c-style vararg functions [cppcoreguidelines-pro-type-vararg]
printf("Failed to create RAM file %s\n", treefile);
^
src/ramcore/SamToNTuple.cxx
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| ramcore::SamParser parser; | ||
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| int64_t mapped_count = 0; |
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warning: no header providing "int64_t" is directly included [misc-include-cleaner]
int64_t mapped_count = 0;
^
src/ramcore/SamToNTuple.cxx
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| int64_t mapped_count = 0; | ||
| int32_t last_refid = -2; |
There was a problem hiding this comment.
warning: no header providing "int32_t" is directly included [misc-include-cleaner]
int32_t last_refid = -2;
^| #include <filesystem> | ||
| #include <Rtypes.h> | ||
| #include <regex> | ||
| #include "../tools/ramview.cxx" |
There was a problem hiding this comment.
warning: included header regex is not used directly [misc-include-cleaner]
| #include "../tools/ramview.cxx" | |
| #include "../tools/ramview.cxx" |
| #include <filesystem> | ||
| #include <Rtypes.h> | ||
| #include <regex> | ||
| #include "../tools/ramview.cxx" |
There was a problem hiding this comment.
warning: suspicious #include of file with '.cxx' extension [bugprone-suspicious-include]
#include "../tools/ramview.cxx"
^
test/ramcoretests.cxx
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| testing::internal::GetCapturedStdout(); | ||
| testing::internal::CaptureStdout(); | ||
| ramview(ttreeFile, region, true, false, nullptr); |
There was a problem hiding this comment.
warning: argument comment missing for literal argument 'cache' [bugprone-argument-comment]
| ramview(ttreeFile, region, true, false, nullptr); | |
| ramview(ttreeFile, region, /*cache=*/true, false, nullptr); |
test/ramcoretests.cxx
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| testing::internal::GetCapturedStdout(); | ||
| testing::internal::CaptureStdout(); | ||
| ramview(ttreeFile, region, true, false, nullptr); |
There was a problem hiding this comment.
warning: argument comment missing for literal argument 'perfstats' [bugprone-argument-comment]
| ramview(ttreeFile, region, true, false, nullptr); | |
| ramview(ttreeFile, region, true, /*perfstats=*/false, nullptr); |
Codecov Report❌ Patch coverage is ❌ Your patch status has failed because the patch coverage (42.85%) 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 +/- ##
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| #include <cstring> | ||
| #include <iostream> | ||
| #include <limits> | ||
| #include <string> |
There was a problem hiding this comment.
warning: included header limits is not used directly [misc-include-cleaner]
| #include <string> | |
| #include <string> |
src/ramcore/SamToNTuple.cxx
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| #include <TFile.h> | ||
| #include <TROOT.h> | ||
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| #include <cstdint> |
There was a problem hiding this comment.
warning: #includes are not sorted properly [llvm-include-order]
#include <cstdint>
^this fix will not be applied because it overlaps with another fix
test/ramcoretests.cxx
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| testing::internal::GetCapturedStdout(); | ||
| testing::internal::CaptureStdout(); | ||
| ramview(ttreeFile, region, /*cache=*/true, /*perfstats=*/false, nullptr); |
There was a problem hiding this comment.
warning: argument comment missing for literal argument 'perfstatsfilename' [bugprone-argument-comment]
| ramview(ttreeFile, region, /*cache=*/true, /*perfstats=*/false, nullptr); | |
| ramview(ttreeFile, region, /*cache=*/true, /*perfstats=*/false, /*perfstatsfilename=*/nullptr); |
test/ramcoretests.cxx
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| testing::internal::GetCapturedStdout(); | ||
| testing::internal::CaptureStdout(); | ||
| ramview(ttreeFile, region, /*cache=*/true, /*perfstats=*/false, nullptr); | ||
| std::string ramview_output = testing::internal::GetCapturedStdout(); |
There was a problem hiding this comment.
warning: no header providing "std::string" is directly included [misc-include-cleaner]
test/ramcoretests.cxx:11:
+ #include <string>
test/ramcoretests.cxx
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| testing::internal::GetCapturedStdout(); | ||
| testing::internal::CaptureStdout(); | ||
| ramview(ttreeFile, region, /*cache=*/true, /*perfstats=*/false, nullptr); | ||
| std::string ramview_output = testing::internal::GetCapturedStdout(); |
There was a problem hiding this comment.
warning: variable 'ramview_output' is not initialized [cppcoreguidelines-init-variables]
| std::string ramview_output = testing::internal::GetCapturedStdout(); | |
| std::string ramview_output = 0 = testing::internal::GetCapturedStdout(); |
test/ramcoretests.cxx
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| } | ||
| testing::internal::CaptureStdout(); | ||
| ramntupleview(rntupleFile, region, /*cache=*/true, /*perfstats=*/false, nullptr); | ||
| std::string ramntupleview_output = testing::internal::GetCapturedStdout(); |
There was a problem hiding this comment.
warning: variable 'ramntupleview_output' is not initialized [cppcoreguidelines-init-variables]
| std::string ramntupleview_output = testing::internal::GetCapturedStdout(); | |
| std::string ramntupleview_output = 0 = testing::internal::GetCapturedStdout(); |
| #include <string> | ||
| #include <cstring> | ||
| #include <vector> | ||
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There was a problem hiding this comment.
warning: included header vector is not used directly [misc-include-cleaner]
tools/samtoramntuple.cxx
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| do_split = true; | ||
| } else if (arg == "-only") { | ||
| if (i + 1 < argc) { | ||
| only_chromosomes.emplace_back(argv[++i]); |
There was a problem hiding this comment.
warning: do not use pointer arithmetic [cppcoreguidelines-pro-bounds-pointer-arithmetic]
only_chromosomes.emplace_back(argv[++i]);
^
| #include "ramcore/SamParser.h" | ||
| #include "rntuple/RAMNTupleRecord.h" | ||
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| #include <cstdint> |
There was a problem hiding this comment.
warning: #includes are not sorted properly [llvm-include-order]
#include <cstdint>
^this fix will not be applied because it overlaps with another fix
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| #include <cstdint> | ||
| #include <map> | ||
| #include <memory> |
There was a problem hiding this comment.
warning: included header map is not used directly [misc-include-cleaner]
| #include <memory> | |
| #include <memory> |
src/ramcore/SamToNTuple.cxx
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| #include <cstdint> | ||
| #include <map> | ||
| #include <memory> | ||
| #include <cstdio> |
There was a problem hiding this comment.
warning: included header memory is not used directly [misc-include-cleaner]
| #include <cstdio> | |
| #include <cstdio> |
src/ramcore/SamToNTuple.cxx
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| #include <memory> | ||
| #include <cstdio> | ||
| #include <thread> | ||
| #include <vector> |
There was a problem hiding this comment.
warning: included header thread is not used directly [misc-include-cleaner]
| #include <vector> | |
| #include <vector> |
| #include <cstdio> | ||
| #include <thread> | ||
| #include <vector> | ||
| #include <mutex> |
There was a problem hiding this comment.
warning: included header vector is not used directly [misc-include-cleaner]
| #include <mutex> | |
| #include <mutex> |
| #include <mutex> | ||
| #include <algorithm> | ||
| #include <unordered_set> | ||
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There was a problem hiding this comment.
warning: included header unordered_set is not used directly [misc-include-cleaner]
src/ramcore/SamToNTuple.cxx
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| 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, |
There was a problem hiding this comment.
warning: function 'samtoramntuple' can be made static or moved into an anonymous namespace to enforce internal linkage [misc-use-internal-linkage]
| 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, |
| const int32_t POS_INTERVAL = 10000; | ||
| const int64_t MAPPED_INTERVAL = 100; | ||
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| auto header_callback = [&headers](const std::string &tag, const std::string &content) { |
There was a problem hiding this comment.
warning: no header providing "std::string" is directly included [misc-include-cleaner]
src/ramcore/SamToNTuple.cxx:9:
- #include <vector>
+ #include <string>
+ #include <vector>| if (sn_pos != std::string::npos) { | ||
| sn_pos += 3; | ||
| size_t tab_pos = content.find('\t', sn_pos); | ||
| std::string ref_name = |
There was a problem hiding this comment.
warning: variable 'ref_name' is not initialized [cppcoreguidelines-init-variables]
| std::string ref_name = | |
| std::string ref_name = 0 = |
src/ramcore/SamToNTuple.cxx
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| }; | ||
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| if (!parser.ParseFile(datafile, header_callback, record_callback)) { | ||
| printf("Failed to parse SAM file %s\n", datafile); |
There was a problem hiding this comment.
warning: do not call c-style vararg functions [cppcoreguidelines-pro-type-vararg]
printf("Failed to parse SAM file %s\n", datafile);
^Signed-off-by: AdityaPandeyCN <adityapand3y666@gmail.com>
| #include <cstdio> | ||
| #include <map> | ||
| #include <memory> | ||
| #include <mutex> |
There was a problem hiding this comment.
warning: included header memory is not used directly [misc-include-cleaner]
| #include <mutex> | |
| #include <mutex> |
| #include <mutex> | ||
| #include <string> | ||
| #include <thread> | ||
| #include <unordered_set> |
There was a problem hiding this comment.
warning: included header thread is not used directly [misc-include-cleaner]
| #include <unordered_set> | |
| #include <unordered_set> |
| #include <string> | ||
| #include <thread> | ||
| #include <unordered_set> | ||
| #include <vector> |
There was a problem hiding this comment.
warning: included header unordered_set is not used directly [misc-include-cleaner]
| #include <vector> | |
| #include <vector> |
| #include <thread> | ||
| #include <unordered_set> | ||
| #include <vector> | ||
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There was a problem hiding this comment.
warning: included header vector is not used directly [misc-include-cleaner]
| 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, |
There was a problem hiding this comment.
warning: function 'samtoramntuple' can be made static or moved into an anonymous namespace to enforce internal linkage [misc-use-internal-linkage]
| 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, |
| if (!std::filesystem::exists("samexample.sam")) { | ||
| GenerateSAMFile("samexample.sam", num_reads_for_test); | ||
| } | ||
| void SetUp() override |
There was a problem hiding this comment.
warning: method 'SetUp' can be made static [readability-convert-member-functions-to-static]
| void SetUp() override | |
| static void SetUp() override |
| std::remove("test_ttree.root"); | ||
| std::remove("test_rntuple.root"); | ||
| } | ||
| void TearDown() override |
There was a problem hiding this comment.
warning: method 'TearDown' can be made static [readability-convert-member-functions-to-static]
| void TearDown() override | |
| static void TearDown() override |
| } | ||
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| TEST_F(ramcoreTest, RNTupleView) | ||
| TEST_F(ramcoreTest, ConversionProducesEqualEntries) |
There was a problem hiding this comment.
warning: function 'TEST_F' can be made static or moved into an anonymous namespace to enforce internal linkage [misc-use-internal-linkage]
| TEST_F(ramcoreTest, ConversionProducesEqualEntries) | |
| TEST_Fstatic (ramcoreTest, ConversionProducesEqualEntries) |
| } | ||
| testing::internal::CaptureStdout(); | ||
| ramview(ttreeFile, region, /*cache=*/true, /*perfstats=*/false, /*perfstatsfilename=*/nullptr); | ||
| std::string ramview_output; |
There was a problem hiding this comment.
warning: variable 'ramview_output' is not initialized [cppcoreguidelines-init-variables]
| std::string ramview_output; | |
| std::string ramview_output = 0; |
| 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; |
There was a problem hiding this comment.
warning: variable 'ramntupleview_output' is not initialized [cppcoreguidelines-init-variables]
| std::string ramntupleview_output; | |
| std::string ramntupleview_output = 0; |
AdityaPandeyCN
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| int main(int argc, char *argv[]) | ||
| { | ||
| if (argc < 2) { | ||
| std::cout << "Usage: " << argv[0] << " <input.sam> [output]\n"; |
There was a problem hiding this comment.
warning: do not use pointer arithmetic [cppcoreguidelines-pro-bounds-pointer-arithmetic]
std::cout << "Usage: " << argv[0] << " <input.sam> [output]\n";
^| output = argv[i]; | ||
| } | ||
| } | ||
| const char *input = argv[1]; |
There was a problem hiding this comment.
warning: do not use pointer arithmetic [cppcoreguidelines-pro-bounds-pointer-arithmetic]
const char *input = argv[1];
^| return 0; | ||
| } | ||
| for (int i = 2; i < argc; i++) { | ||
| std::string arg = argv[i]; |
There was a problem hiding this comment.
warning: do not use pointer arithmetic [cppcoreguidelines-pro-bounds-pointer-arithmetic]
std::string arg = argv[i];
^| } else if (arg == "-only") { | ||
| if (i + 1 < argc) { | ||
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| only_chromosomes.emplace_back(argv[++i]); |
There was a problem hiding this comment.
warning: do not use pointer arithmetic [cppcoreguidelines-pro-bounds-pointer-arithmetic]
only_chromosomes.emplace_back(argv[++i]);
^| } | ||
| } else if (arg == "-noindex") { | ||
| do_index = false; | ||
| } else if (arg == "-illumina") { |
There was a problem hiding this comment.
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") {
^| } else if (arg == "-dropqual") { | ||
| quality_mode = RAMNTupleRecord::kDrop; | ||
| } else if (arg[0] != '-') { | ||
| output = argv[i]; |
There was a problem hiding this comment.
warning: do not use pointer arithmetic [cppcoreguidelines-pro-bounds-pointer-arithmetic]
output = argv[i];
^| } | ||
| } | ||
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| std::string outfile; |
There was a problem hiding this comment.
warning: variable 'outfile' is not initialized [cppcoreguidelines-init-variables]
| std::string outfile; | |
| std::string outfile = 0; |
| } | ||
| samtoramntuple(input, ramfile.c_str(), do_index, true, true, 505, quality_mode); | ||
| } | ||
| } catch (const std::exception &e) { |
There was a problem hiding this comment.
warning: no header providing "std::exception" is directly included [misc-include-cleaner]
tools/samtoramntuple.cxx:2:
- #include <iostream>
+ #include <exception>
+ #include <iostream>2 participants
This PR addresses:-