TEST(BamHeaderTest, ExtractFromRawDataOk)
{
ReadGroupInfo rg1("rg1");
rg1.Sample("control");
ReadGroupInfo rg2("rg2");
rg2.Sample("condition1");
ReadGroupInfo rg3("rg3");
rg3.Sample("condition1");
SequenceInfo seq1("chr1");
seq1.Length("2038").Species("chocobo");
SequenceInfo seq2("chr2");
seq2.Length("3042").Species("chocobo");
ProgramInfo prog1("_foo_");
prog1.Name("ide");
BamHeader header;
header.Version("1.1")
.SortOrder("queryname")
.PacBioBamVersion("3.0.1")
.AddReadGroup(rg1)
.AddReadGroup(rg2)
.AddReadGroup(rg3)
.AddSequence(seq1)
.AddSequence(seq2)
.AddProgram(prog1)
.AddComment("ipsum and so on")
.AddComment("citation needed");
const string& expectedText = "@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\tPL:PACBIO\tDS:READTYPE=UNKNOWN\tSM:control\tPM:SEQUEL\n"
"@RG\tID:rg2\tPL:PACBIO\tDS:READTYPE=UNKNOWN\tSM:condition1\tPM:SEQUEL\n"
"@RG\tID:rg3\tPL:PACBIO\tDS:READTYPE=UNKNOWN\tSM:condition1\tPM:SEQUEL\n"
"@PG\tID:_foo_\tPN:ide\n"
"@CO\tipsum and so on\n"
"@CO\tcitation needed\n";
string text = header.ToSam();
PBBAM_SHARED_PTR<bam_hdr_t> rawData(sam_hdr_parse(text.size(), text.c_str()), tests::BamHdrDeleter());
rawData->ignore_sam_err = 0;
rawData->cigar_tab = NULL;
rawData->l_text = text.size();
rawData->text = (char*)calloc(rawData->l_text + 1, 1);
memcpy(rawData->text, text.c_str(), rawData->l_text);
const BamHeader newHeader = BamHeader(string(rawData->text, rawData->l_text));
EXPECT_EQ(header.Version(), newHeader.Version());
EXPECT_EQ(header.SortOrder(), newHeader.SortOrder());
EXPECT_EQ(header.PacBioBamVersion(), newHeader.PacBioBamVersion());
text = newHeader.ToSam();
EXPECT_EQ(expectedText, text);
}
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);
}
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));
}
