Add tests for SamParser and RAMNTupleUtils to improve coverage (fixes…

test/CMakeLists.txt

@@ -36,3 +36,4 @@ install(TARGETS ramcoretests chromosome_split_test
     RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
 )
 
+add_ramcore_test(samparsertest samparsertest.cxx)

test/samparsertest.cxx

@@ -0,0 +1,246 @@
+#include <gtest/gtest.h>
+#include <fstream>
+#include <cstdio>
+#include <string>
+#include <vector>
+
+#include "ramcore/SamParser.h"
+#include "rntuple/RAMNTupleRecord.h"
+
+// ─────────────────────────────────────────────────────────────────────────────
+// Helpers
+// ─────────────────────────────────────────────────────────────────────────────
+
+static void WriteSAM(const char *path, const std::string &content)
+{
+   std::ofstream f(path);
+   f << content;
+}
+
+// ─────────────────────────────────────────────────────────────────────────────
+// SamParser tests
+// ─────────────────────────────────────────────────────────────────────────────
+
+namespace {
+
+class SamParserTest : public ::testing::Test {
+protected:
+   const char *kSamFile = "parser_test.sam";
+   void TearDown() override { std::remove(kSamFile); }
+};
+
+/// Parser must return false for a non-existent file.
+TEST_F(SamParserTest, NonExistentFileReturnsFalse)
+{
+   ramcore::SamParser parser;
+   bool ok = parser.ParseFile("no_such_file.sam", nullptr, nullptr);
+   EXPECT_FALSE(ok);
+}
+
+/// Header lines starting with '@' must trigger the header callback.
+TEST_F(SamParserTest, HeaderCallbackFired)
+{
+   WriteSAM(kSamFile,
+            "@HD\tVN:1.6\tSO:coordinate\n"
+            "@SQ\tSN:chr1\tLN:248956422\n");
+
+   ramcore::SamParser parser;
+   std::vector<std::string> tags;
+   parser.ParseFile(kSamFile,
+      [&](const std::string &tag, const std::string &) { tags.push_back(tag); },
+      nullptr);
+
+   ASSERT_EQ(tags.size(), 2u);
+   EXPECT_EQ(tags[0], "@HD");
+   EXPECT_EQ(tags[1], "@SQ");
+}
+
+/// Record callback must fire once per alignment line.
+TEST_F(SamParserTest, RecordCallbackFiredForEachAlignment)
+{
+   WriteSAM(kSamFile,
+            "@HD\tVN:1.6\n"
+            "read1\t0\tchr1\t100\t60\t10M\t*\t0\t0\tACGTACGTAC\t*\n"
+            "read2\t16\tchr1\t200\t60\t10M\t*\t0\t0\tACGTACGTAC\t*\n");
+
+   ramcore::SamParser parser;
+   size_t count = 0;
+   parser.ParseFile(kSamFile, nullptr,
+      [&](const ramcore::SamRecord &, size_t) { ++count; });
+
+   EXPECT_EQ(count, 2u);
+   EXPECT_EQ(parser.GetRecordsProcessed(), 2u);
+}
+
+/// Parsed record fields must match the SAM columns exactly.
+TEST_F(SamParserTest, RecordFieldsParsedCorrectly)
+{
+   WriteSAM(kSamFile,
+            "@HD\tVN:1.6\n"
+            "myread\t99\tchr2\t500\t30\t5M2I3M\t=\t600\t110\tACGTACGTAC\tIIIIIIIIII\n");
+
+   ramcore::SamParser parser;
+   ramcore::SamRecord captured;
+   parser.ParseFile(kSamFile, nullptr,
+      [&](const ramcore::SamRecord &rec, size_t) { captured = rec; });
+
+   EXPECT_EQ(captured.qname,  "myread");
+   EXPECT_EQ(captured.flag,   99);
+   EXPECT_EQ(captured.rname,  "chr2");
+   EXPECT_EQ(captured.pos,    500);
+   EXPECT_EQ(captured.mapq,   30);
+   EXPECT_EQ(captured.cigar,  "5M2I3M");
+   EXPECT_EQ(captured.rnext,  "=");
+   EXPECT_EQ(captured.pnext,  600);
+   EXPECT_EQ(captured.tlen,   110);
+   EXPECT_EQ(captured.seq,    "ACGTACGTAC");
+   EXPECT_EQ(captured.qual,   "IIIIIIIIII");
+}
+
+/// An empty SAM file (no headers, no records) must parse successfully.
+TEST_F(SamParserTest, EmptyFileParseSucceeds)
+{
+   WriteSAM(kSamFile, "");
+   ramcore::SamParser parser;
+   bool ok = parser.ParseFile(kSamFile, nullptr, nullptr);
+   EXPECT_TRUE(ok);
+   EXPECT_EQ(parser.GetRecordsProcessed(), 0u);
+}
+
+/// A SAM file with only headers and no records must produce zero record calls.
+TEST_F(SamParserTest, HeaderOnlyFileProducesNoRecords)
+{
+   WriteSAM(kSamFile,
+            "@HD\tVN:1.6\n"
+            "@SQ\tSN:chr1\tLN:1000\n");
+
+   ramcore::SamParser parser;
+   size_t count = 0;
+   parser.ParseFile(kSamFile, nullptr,
+      [&](const ramcore::SamRecord &, size_t) { ++count; });
+
+   EXPECT_EQ(count, 0u);
+}
+
+/// Optional fields must be captured in the record.
+TEST_F(SamParserTest, OptionalFieldsCaptured)
+{
+   WriteSAM(kSamFile,
+            "@HD\tVN:1.6\n"
+            "read1\t0\tchr1\t100\t60\t10M\t*\t0\t0\tACGTACGTAC\t*\tNM:i:0\tRG:Z:sample1\n");
+
+   ramcore::SamParser parser;
+   ramcore::SamRecord captured;
+   parser.ParseFile(kSamFile, nullptr,
+      [&](const ramcore::SamRecord &rec, size_t) { captured = rec; });
+
+   EXPECT_GE(captured.optional_fields.size(), 1u);
+}
+
+/// Lines processed counter must include both header and record lines.
+TEST_F(SamParserTest, LinesProcessedCountIsCorrect)
+{
+   WriteSAM(kSamFile,
+            "@HD\tVN:1.6\n"
+            "@SQ\tSN:chr1\tLN:1000\n"
+            "read1\t0\tchr1\t100\t60\t10M\t*\t0\t0\tACGTACGTAC\t*\n");
+
+   ramcore::SamParser parser;
+   parser.ParseFile(kSamFile, nullptr, nullptr);
+   EXPECT_EQ(parser.GetLinesProcessed(), 3u);
+}
+
+/// StripCRLF must remove trailing CR and LF characters.
+TEST(StripCRLFTest, RemovesTrailingCRLF)
+{
+   char buf1[] = "hello\r\n";
+   ramcore::StripCRLF(buf1);
+   EXPECT_STREQ(buf1, "hello");
+
+   char buf2[] = "world\n";
+   ramcore::StripCRLF(buf2);
+   EXPECT_STREQ(buf2, "world");
+
+   char buf3[] = "noend";
+   ramcore::StripCRLF(buf3);
+   EXPECT_STREQ(buf3, "noend");
+}
+
+// ─────────────────────────────────────────────────────────────────────────────
+// RAMNTupleUtils encode/decode tests
+// ─────────────────────────────────────────────────────────────────────────────
+
+/// EncodeSequence + DecodeSequence must be inverse operations.
+TEST(RAMNTupleUtilsTest, SequenceRoundTrip)
+{
+   const std::string original = "ACGTACGTACGT";
+   std::string encoded = RAMNTupleUtils::EncodeSequence(original);
+
+   // Encoded format: 4-byte length prefix + packed nibbles
+   ASSERT_GE(encoded.size(), 4u);
+   uint32_t stored_len = 0;
+   std::memcpy(&stored_len, encoded.data(), 4);
+   EXPECT_EQ(stored_len, original.size());
+
+   std::string decoded = RAMNTupleUtils::DecodeSequence(encoded.substr(4), original.size());
+   EXPECT_EQ(decoded, original);
+}
+
+/// Odd-length sequences must round-trip correctly.
+TEST(RAMNTupleUtilsTest, OddLengthSequenceRoundTrip)
+{
+   const std::string original = "ACGTA";
+   std::string encoded = RAMNTupleUtils::EncodeSequence(original);
+   std::string decoded = RAMNTupleUtils::DecodeSequence(encoded.substr(4), original.size());
+   EXPECT_EQ(decoded, original);
+}
+
+/// Empty sequence must encode and decode without crashing.
+TEST(RAMNTupleUtilsTest, EmptySequenceRoundTrip)
+{
+   const std::string original = "";
+   std::string encoded = RAMNTupleUtils::EncodeSequence(original);
+   std::string decoded = RAMNTupleUtils::DecodeSequence(encoded.substr(4), 0);
+   EXPECT_EQ(decoded, original);
+}
+
+/// EncodeQuality + DecodeQuality must be inverse for default Phred33 mode.
+TEST(RAMNTupleUtilsTest, QualityRoundTripPhred33)
+{
+   const std::string original = "IIIIIIIIII";
+   uint32_t flags = RAMNTupleRecord::kPhred33;
+   std::string encoded = RAMNTupleUtils::EncodeQuality(original, flags);
+   std::string decoded = RAMNTupleUtils::DecodeQuality(encoded, flags);
+   EXPECT_EQ(decoded, original);
+}
+
+/// Quality scores must round-trip when drop mode is used.
+TEST(RAMNTupleUtilsTest, QualityRoundTripDropMode)
+{
+   const std::string original = "IIIIIIIIII";
+   uint32_t flags = RAMNTupleRecord::kDrop;
+   std::string encoded = RAMNTupleUtils::EncodeQuality(original, flags);
+   // In drop mode decoded quality should be empty or placeholder
+   std::string decoded = RAMNTupleUtils::DecodeQuality(encoded, flags);
+   // Just verify no crash and result is a string
+   EXPECT_NO_THROW(RAMNTupleUtils::DecodeQuality(encoded, flags));
+}
+
+/// ParseCIGAR + FormatCIGAR must be inverse operations.
+TEST(RAMNTupleUtilsTest, CIGARRoundTrip)
+{
+   const std::string original = "10M2I5M3D";
+   auto ops = RAMNTupleUtils::ParseCIGAR(original);
+   EXPECT_FALSE(ops.empty());
+   std::string formatted = RAMNTupleUtils::FormatCIGAR(ops);
+   EXPECT_EQ(formatted, original);
+}
+
+/// Wildcard CIGAR '*' must parse without crashing.
+TEST(RAMNTupleUtilsTest, WildcardCIGARParsesCleanly)
+{
+   auto ops = RAMNTupleUtils::ParseCIGAR("*");
+   EXPECT_TRUE(ops.empty());
+}
+
+} // namespace