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);
}
void Interval(const BamHeader& header,
const GenomicInterval& interval)
{
htsIterator_.reset(nullptr);
if (header.HasSequence(interval.Name())) {
auto id = header.SequenceId(interval.Name());
if (id >= 0 && static_cast<size_t>(id) < header.NumSequences()) {
htsIterator_.reset(bam_itr_queryi(htsIndex_.get(),
id,
interval.Start(),
interval.Stop()));
}
}
if (!htsIterator_)
throw std::runtime_error("could not create iterator for requested region");
}
