def test_indel_consensus_case_3():
'''
test consensus.indel_consensus() with identical record between freebayes/samtools
Parameters
---------
Returns
-------
'''
chrom, pos, ref, alt, record = _get_test_record()
test_record = {(chrom, pos, ref, alt): record}
freebayes = test_record
rtg = []
samtools = test_record
consensus_data = consensus.indel_consensus(freebayes, rtg, samtools)
consensus_data = pd.DataFrame(consensus_data,
columns=["chrom", "pos", "ref", "alt", "id_counter", "qual", "filter", "nr", "na",
"nd"]
)
consensus_data = consensus_data.astype({"chrom": "str"})
assert not consensus_data[(consensus_data.pos == pos) & (consensus_data["chrom"] == chrom)].empty
def test_indel_consensus_case_4():
'''
test consensus.snv_consensus() with empty data
Parameters
testdir: str directory
---------
Returns
-------
'''
consensus_data = consensus.indel_consensus([], [], [])
assert consensus_data == []
def test_indel_consensus_case_5():
'''
test consensus.snv_consensus() with no shared records
Parameters
testdir: str directory
---------
Returns
-------
'''
chrom, pos, ref, alt, record = _get_test_record()
samtools = {(chrom, pos + 2, ref, alt): record}
freebayes = {(chrom, pos + 3, ref, alt): record}
rtg = {(chrom, pos + 4, ref, alt): record}
consensus_data = consensus.indel_consensus(samtools, freebayes, rtg)
assert consensus_data == []