C++ (Cpp) BamHeader::Program Examples

Example #1

File: test_BamHeader.cpp Project: PacificBiosciences/pbbam

TEST(BamHeaderTest, DefaultConstruction)
{
    BamHeader header;
    EXPECT_TRUE(header.Version().empty());
    EXPECT_TRUE(header.SortOrder().empty()); // default to unknown ?
    EXPECT_TRUE(header.ReadGroups().empty());
    EXPECT_TRUE(header.Sequences().empty());
    EXPECT_TRUE(header.Programs().empty());
    EXPECT_TRUE(header.Comments().empty());

    EXPECT_THROW(header.Program("foo"),     std::exception);
    EXPECT_THROW(header.ReadGroup("foo"),   std::exception);
    EXPECT_THROW(header.SequenceId("foo"),  std::exception);
    EXPECT_THROW(header.SequenceLength(42), std::exception);
    EXPECT_THROW(header.SequenceName(42),   std::exception);
}

Example #2

File: test_BamHeader.cpp Project: PacificBiosciences/pbbam

TEST(BamHeaderTest, DecodeTest)
{
    const string& text = "@HD\tVN:1.1\tSO:queryname\tpb:3.0.1\n"
                         "@SQ\tSN:chr1\tLN:2038\tSP:chocobo\n"
                         "@SQ\tSN:chr2\tLN:3042\tSP:chocobo\n"
                         "@RG\tID:rg1\tSM:control\n"
                         "@RG\tID:rg2\tSM:condition1\n"
                         "@RG\tID:rg3\tSM:condition1\n"
                         "@PG\tID:_foo_\tPN:ide\n"
                         "@CO\tipsum and so on\n"
                         "@CO\tcitation needed\n";

    BamHeader header = BamHeader(text);

    EXPECT_EQ(string("1.1"),       header.Version());
    EXPECT_EQ(string("queryname"), header.SortOrder());
    EXPECT_EQ(string("3.0.1"),     header.PacBioBamVersion());

    EXPECT_EQ(3, header.ReadGroups().size());
    EXPECT_TRUE(header.HasReadGroup("rg1"));
    EXPECT_TRUE(header.HasReadGroup("rg2"));
    EXPECT_TRUE(header.HasReadGroup("rg3"));

    EXPECT_EQ(string("control"),    header.ReadGroup("rg1").Sample());
    EXPECT_EQ(string("condition1"), header.ReadGroup("rg2").Sample());
    EXPECT_EQ(string("condition1"), header.ReadGroup("rg3").Sample());

    EXPECT_EQ(2, header.Sequences().size());
    EXPECT_TRUE(header.HasSequence("chr1"));
    EXPECT_TRUE(header.HasSequence("chr2"));
    EXPECT_EQ(string("chocobo"), header.Sequence("chr1").Species());
    EXPECT_EQ(string("chocobo"), header.Sequence("chr2").Species());
    EXPECT_EQ(string("2038"), header.Sequence("chr1").Length());
    EXPECT_EQ(string("3042"), header.Sequence("chr2").Length());

    EXPECT_EQ(1, header.Programs().size());
    EXPECT_TRUE(header.HasProgram("_foo_"));
    EXPECT_EQ(string("ide"), header.Program("_foo_").Name());

    EXPECT_EQ(2, header.Comments().size());
    EXPECT_EQ(string("ipsum and so on"), header.Comments().at(0));
    EXPECT_EQ(string("citation needed"), header.Comments().at(1));
}