Skip to content

Chore clang-tidy warnings for ramcoretests.cxx #48

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Draft
RedBlueBird wants to merge 4 commits into
base: develop
Choose a base branch
from
Draft

Chore clang-tidy warnings for ramcoretests.cxx #48

Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
3954850
fix bugprone argument comment warnings
RedBlueBird Mar 24, 2026
d580661
fix includes warnings
RedBlueBird Mar 24, 2026
dac7b07
fix includes order warnings
RedBlueBird Mar 24, 2026
ae1fd5f
fixes other clang-tidy warnings
RedBlueBird Mar 24, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
122 changes: 79 additions & 43 deletions test/ramcoretests.cxx
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,29 +1,29 @@
#include "../benchmark/generate_sam_benchmark.h"
#include "../tools/ramview.cxx"
Copy link
Copy Markdown

@github-actions github-actions Bot Mar 24, 2026

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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

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

#include "ramcore/RAMNTupleView.h"
#include "ramcore/SamToNTuple.h"
#include "ramcore/SamToTTree.h"
#include "rntuple/RAMNTupleRecord.h"
#include <gtest/gtest.h>
#include <ROOT/RNTupleReader.hxx>
#include <ROOT/RNTupleView.hxx>
#include <Rtypes.h>
#include <RtypesCore.h>
#include <TFile.h>
#include <TTree.h>
#include <cstdint>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include <filesystem>
#include <fstream>
#include <iostream>
#include <memory>
#include <string>
#include "../benchmark/generate_sam_benchmark.h"
#include "../tools/ramview.cxx"
#include "ramcore/RAMNTupleView.h"
#include "ramcore/SamToNTuple.h"
#include "rntuple/RAMNTupleRecord.h"
#include "ramcore/SamToTTree.h"
namespace {

class ramcoreTest : public ::testing::Test {
protected:
void SetUp() override {
GenerateSAMFile("samexample.sam", 100);
GenerateSAMFile("samexample.sam", /*num_reads=*/100);
std::remove("test_ttree.root");
std::remove("test_rntuple.root");
}
Expand All @@ -41,17 +41,19 @@ TEST_F(ramcoreTest, ConversionProducesEqualEntries) {
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(samFile, ttreeFile, /*index=*/true, /*split=*/true, /*cache=*/true,
/*compression_algorithm=*/1, /*quality_policy=*/0);
samtoramntuple(samFile, rntupleFile, /*index=*/true, /*split=*/true, /*cache=*/true,
/*compression_algorithm=*/505, /*quality_policy=*/0);

auto ft = std::unique_ptr<TFile>(TFile::Open(ttreeFile));
ASSERT_TRUE(ft && !ft->IsZombie());

auto ttree = dynamic_cast<TTree *>(ft->Get("RAM"));
auto *ttree = dynamic_cast<TTree *>(ft->Get("RAM"));
Long64_t ttreeEntries = ttree->GetEntries();

auto reader = ROOT::RNTupleReader::Open("RAM", rntupleFile);
Long64_t rntupleEntries = reader->GetNEntries();
auto rntupleEntries = static_cast<Long64_t>(reader->GetNEntries());

EXPECT_EQ(ttreeEntries, rntupleEntries);
EXPECT_EQ(ttreeEntries, 100);
Expand All @@ -60,49 +62,63 @@ TEST_F(ramcoreTest, ConversionProducesEqualEntries) {
TEST_F(ramcoreTest, RNTupleViewRegionQueries)
{
const char *rntupleFile = "test_rntuple.root";
samtoramntuple("samexample.sam", rntupleFile, true, true, true, 505, 0);
samtoramntuple(/*datafile=*/"samexample.sam", rntupleFile, /*index=*/true, /*split=*/true,
/*cache=*/true, /*compression_algorithm=*/505, /*quality_policy=*/0);

Long64_t hit = ramntupleview(rntupleFile, "chr1:1-1000000", true, false, nullptr);
Long64_t hit = ramntupleview(rntupleFile, /*query=*/"chr1:1-1000000", /*cache=*/true,
/*perfstats=*/false, /*perfstatsfilename=*/nullptr);
EXPECT_GE(hit, 0);

Long64_t miss = ramntupleview(rntupleFile, "chrNonExistent:1-100", true, false, nullptr);
Long64_t miss = ramntupleview(rntupleFile, /*query=*/"chrNonExistent:1-100", /*cache=*/true,
/*perfstats=*/false, /*perfstatsfilename=*/nullptr);
EXPECT_EQ(miss, 0);

Long64_t wildcard = ramntupleview(rntupleFile, "*", true, false, nullptr);
Long64_t wildcard = ramntupleview(rntupleFile, /*query=*/"*", /*cache=*/true,
/*perfstats=*/false, /*perfstatsfilename=*/nullptr);
EXPECT_EQ(wildcard, 100);

Long64_t empty = ramntupleview(rntupleFile, "", true, false, nullptr);
Long64_t empty = ramntupleview(rntupleFile, /*query=*/"", /*cache=*/true,
/*perfstats=*/false, /*perfstatsfilename=*/nullptr);
EXPECT_EQ(empty, 100);

Long64_t null = ramntupleview(rntupleFile, nullptr, true, false, nullptr);
Long64_t null = ramntupleview(rntupleFile, /*query=*/nullptr, /*cache=*/true,
/*perfstats=*/false, /*perfstatsfilename=*/nullptr);
EXPECT_EQ(null, 100);

Long64_t whole = ramntupleview(rntupleFile, "chr1", true, false, nullptr);
Long64_t whole = ramntupleview(rntupleFile, /*query=*/"chr1", /*cache=*/true,
/*perfstats=*/false, /*perfstatsfilename=*/nullptr);
EXPECT_GE(whole, 0);

Long64_t single = ramntupleview(rntupleFile, "chr1:500", true, false, nullptr);
Long64_t single = ramntupleview(rntupleFile, /*query=*/"chr1:500", /*cache=*/true,
/*perfstats=*/false, /*perfstatsfilename=*/nullptr);
EXPECT_GE(single, 0);

Long64_t invalid = ramntupleview(rntupleFile, "chr1:abc-def", true, false, nullptr);
Long64_t invalid = ramntupleview(rntupleFile, /*query=*/"chr1:abc-def", /*cache=*/true,
/*perfstats=*/false, /*perfstatsfilename=*/nullptr);
EXPECT_EQ(invalid, 0);

Long64_t lateChr = ramntupleview(rntupleFile, "chrX:1-100", true, false, nullptr);
Long64_t lateChr = ramntupleview(rntupleFile, /*query=*/"chrX:1-100", /*cache=*/true,
/*perfstats=*/false, /*perfstatsfilename=*/nullptr);
EXPECT_GE(lateChr, 0);

Long64_t zeroStart = ramntupleview(rntupleFile, "chr1:0-100", true, false, nullptr);
Long64_t zeroStart = ramntupleview(rntupleFile, /*query=*/"chr1:0-100", /*cache=*/true,
/*perfstats=*/false, /*perfstatsfilename=*/nullptr);
EXPECT_GE(zeroStart, 0);
}

TEST_F(ramcoreTest, RNTupleViewOpenFailure)
{
Long64_t count = ramntupleview("nonexistent_file.root", "chr1:1-100", true, false, nullptr);
Long64_t count = ramntupleview(/*file=*/"nonexistent_file.root", /*query=*/"chr1:1-100",
/*cache=*/true, /*perfstats=*/false,
/*perfstatsfilename=*/nullptr);
EXPECT_EQ(count, 0);
}

TEST_F(ramcoreTest, RNTupleDataIntegrity)
{
const char *rntupleFile = "test_rntuple.root";
samtoramntuple("samexample.sam", rntupleFile, true, true, true, 505, 0);
samtoramntuple(/*datafile=*/"samexample.sam", rntupleFile, /*index=*/true, /*split=*/true,
/*cache=*/true, /*compression_algorithm=*/505, /*quality_policy=*/0);

auto reader = ROOT::RNTupleReader::Open("RAM", rntupleFile);
ASSERT_NE(reader, nullptr);
Expand All @@ -125,7 +141,7 @@ TEST_F(ramcoreTest, RNTupleDataIntegrity)
EXPECT_EQ(storedLen, 36);

std::cout << "[ INFO ] Data Integrity - Pos: " << firstPos << ", Encoded Seq Size: " << firstSeq.size()
<< " (Header: " << storedLen << ")" << std::endl;
<< " (Header: " << storedLen << ")" << '\n';
}

TEST_F(ramcoreTest, RNTupleViewCigarOverlap)
Expand All @@ -141,12 +157,21 @@ TEST_F(ramcoreTest, RNTupleViewCigarOverlap)
<< "AAAAAAAAAAAAAAAAAAAA\t*\n";
}

samtoramntuple(customSam, rntupleFile, false, false, false, 505, 0);
samtoramntuple(customSam, rntupleFile, /*index=*/false, /*split=*/false, /*cache=*/false,
/*compression_algorithm=*/505, /*quality_policy=*/0);

EXPECT_EQ(ramntupleview(rntupleFile, "chr1:140-160", true, false, nullptr), 1);
EXPECT_EQ(ramntupleview(rntupleFile, "chr1:201-210", true, false, nullptr), 0);
EXPECT_EQ(ramntupleview(rntupleFile, "chr1:50-110", true, false, nullptr), 1);
EXPECT_EQ(ramntupleview(rntupleFile, "chr1:1-50", true, false, nullptr), 0);
EXPECT_EQ(ramntupleview(rntupleFile, /*query=*/"chr1:140-160", /*cache=*/true,
/*perfstats=*/false, /*perfstatsfilename=*/nullptr),
1);
EXPECT_EQ(ramntupleview(rntupleFile, /*query=*/"chr1:201-210", /*cache=*/true,
/*perfstats=*/false, /*perfstatsfilename=*/nullptr),
0);
EXPECT_EQ(ramntupleview(rntupleFile, /*query=*/"chr1:50-110", /*cache=*/true,
/*perfstats=*/false, /*perfstatsfilename=*/nullptr),
1);
EXPECT_EQ(ramntupleview(rntupleFile, /*query=*/"chr1:1-50", /*cache=*/true,
/*perfstats=*/false, /*perfstatsfilename=*/nullptr),
0);

std::remove(customSam);
std::remove(rntupleFile);
Expand All @@ -168,9 +193,11 @@ TEST_F(ramcoreTest, RNTupleViewFlagFiltering)
sam << "unmapped\t4\tchr1\t100\t0\t50M\t*\t0\t0\t" << seq << "\t*\n";
}

samtoramntuple(customSam, rntupleFile, false, false, false, 505, 0);
samtoramntuple(customSam, rntupleFile, /*index=*/false, /*split=*/false, /*cache=*/false,
/*compression_algorithm=*/505, /*quality_policy=*/0);

Long64_t count = ramntupleview(rntupleFile, "chr1:1-500", true, false, nullptr);
Long64_t count = ramntupleview(rntupleFile, /*query=*/"chr1:1-500", /*cache=*/true,
/*perfstats=*/false, /*perfstatsfilename=*/nullptr);
EXPECT_EQ(count, 1) << "Only primary read should pass FLAG_FILTER";

std::remove(customSam);
Expand Down Expand Up @@ -312,12 +339,15 @@ TEST_F(ramcoreTest, SmartIndexSkipsUnmappedReads)
sam << "mapped2\t0\tchr1\t2000\t60\t50M\t*\t0\t0\t" << std::string(50, 'A') << "\t*\n";
}

samtoramntuple(customSam, rntupleFile, true, false, false, 505, 0);
samtoramntuple(customSam, rntupleFile, /*index=*/true, /*split=*/false, /*cache=*/false,
/*compression_algorithm=*/505, /*quality_policy=*/0);

Long64_t count = ramntupleview(rntupleFile, "chr1:900-2100", true, false, nullptr);
Long64_t count = ramntupleview(rntupleFile, /*query=*/"chr1:900-2100", /*cache=*/true,
/*perfstats=*/false, /*perfstatsfilename=*/nullptr);
EXPECT_EQ(count, 2) << "Both mapped reads should be queryable";

Long64_t unmapped = ramntupleview(rntupleFile, "*:0-100", true, false, nullptr);
Long64_t unmapped = ramntupleview(rntupleFile, /*query=*/"*:0-100", /*cache=*/true,
/*perfstats=*/false, /*perfstatsfilename=*/nullptr);
EXPECT_EQ(unmapped, 0) << "Unmapped reads should not appear in index queries";

std::remove(customSam);
Expand All @@ -342,12 +372,15 @@ TEST_F(ramcoreTest, SmartIndexCreatesEntryAtChromosomeBoundary)
<< "\t*\n";
}

samtoramntuple(customSam, rntupleFile, true, false, false, 505, 0);
samtoramntuple(customSam, rntupleFile, /*index=*/true, /*split=*/false, /*cache=*/false,
/*compression_algorithm=*/505, /*quality_policy=*/0);

Long64_t chr1_hits = ramntupleview(rntupleFile, "chr1:1000-6000", true, false, nullptr);
Long64_t chr1_hits = ramntupleview(rntupleFile, /*query=*/"chr1:1000-6000", /*cache=*/true,
/*perfstats=*/false, /*perfstatsfilename=*/nullptr);
EXPECT_GT(chr1_hits, 0) << "chr1 reads should be queryable";

Long64_t chr2_hits = ramntupleview(rntupleFile, "chr2:500-5500", true, false, nullptr);
Long64_t chr2_hits = ramntupleview(rntupleFile, /*query=*/"chr2:500-5500", /*cache=*/true,
/*perfstats=*/false, /*perfstatsfilename=*/nullptr);
EXPECT_GT(chr2_hits, 0) << "chr2 reads should be immediately queryable at boundary";

std::remove(customSam);
Expand All @@ -370,12 +403,15 @@ TEST_F(ramcoreTest, SmartIndexRespectsPositionInterval)
sam << "far_read\t0\tchr1\t50000\t60\t50M\t*\t0\t0\t" << std::string(50, 'A') << "\t*\n";
}

samtoramntuple(customSam, rntupleFile, true, false, false, 505, 0);
samtoramntuple(customSam, rntupleFile, /*index=*/true, /*split=*/false, /*cache=*/false,
/*compression_algorithm=*/505, /*quality_policy=*/0);

Long64_t cluster = ramntupleview(rntupleFile, "chr1:900-1100", true, false, nullptr);
Long64_t cluster = ramntupleview(rntupleFile, /*query=*/"chr1:900-1100", /*cache=*/true,
/*perfstats=*/false, /*perfstatsfilename=*/nullptr);
EXPECT_EQ(cluster, 200);

Long64_t far = ramntupleview(rntupleFile, "chr1:49900-50100", true, false, nullptr);
Long64_t far = ramntupleview(rntupleFile, /*query=*/"chr1:49900-50100", /*cache=*/true,
/*perfstats=*/false, /*perfstatsfilename=*/nullptr);
EXPECT_EQ(far, 1) << "Distant read should be indexed via position interval";

std::remove(customSam);
Expand Down
Loading