def XXtest_vcf_tabix_index_build_index(reduced_pg_vcf):
tabix.TabixIndex.build(str(reduced_pg_vcf))
assert os.path.exists(str(reduced_pg_vcf) + '.tbi')
idx = tabix.TabixIndex(str(reduced_pg_vcf),
auto_build=False,
auto_load=True,
require_index=True)
assert idx.struct_ptr
assert idx.struct
def XXtest_vcf_tabix_index_auto_load(reduced_pg_vcf, reduced_pg_tbi):
idx = tabix.TabixIndex(str(reduced_pg_vcf), auto_build=False)
assert idx.path == reduced_pg_vcf
assert idx.tbi_path == str(reduced_pg_vcf) + '.tbi'
assert idx.file
assert not idx.require_index
assert idx.auto_load
assert not idx.auto_build
assert idx.struct_ptr
assert idx.struct
def test_vcf_tabix_load_whole_file(reduced_pg_vcf, reduced_pg_tbi):
with tabix.TabixIndex(str(reduced_pg_vcf), require_index=True) as t:
count = 0
for l in t.from_start():
count += 1
assert count == 112
def XXtest_vcf_tabix_index_require_index_fails(reduced_pg_vcf):
with pytest.raises(tabix.TabixIndexException):
tabix.TabixIndex(str(reduced_pg_vcf),
auto_build=False,
auto_load=False,
require_index=True)
def test_vcf_tabix_get_header(reduced_pg_vcf, reduced_pg_tbi):
with tabix.TabixIndex(str(reduced_pg_vcf), require_index=True) as t:
header = t.get_header()
assert header.startswith('##fileformat=VCFv4.1')
assert len(header) == 3598
def test_vcf_tabix_load_chr3_region(reduced_pg_vcf, reduced_pg_tbi):
with tabix.TabixIndex(str(reduced_pg_vcf), require_index=True) as t:
count = 0
for l in t.query('chr3:45,000,000-150,000,000'):
count += 1
assert count == 3