def test_expand_row_with_extra_fields():
header = {"extraFields": slice(3, 8), "readCount": 8, "meanCoverage": 9, "thresholds": {}, "sampleName": 10}
row = BASE_COLS + EXTRA_COLS + SAMBAMBA_COLS + SAMBAMBA_END_COLS
row_data = sambamba.expand_row(header, row)
assert row_data["extraFields"] == EXTRA_COLS
assert row_data["readCount"] == 232
assert row_data["meanCoverage"] == 25.4946
assert row_data["sampleName"] == "ADM992A10"
def test_expand_row_with_extra_fields():
header = {'extraFields': slice(3, 8), 'readCount': 8, 'meanCoverage': 9,
'thresholds': {}, 'sampleName': 10}
row = BASE_COLS + EXTRA_COLS + SAMBAMBA_COLS + SAMBAMBA_END_COLS
row_data = sambamba.expand_row(header, row)
assert row_data['extraFields'] == EXTRA_COLS
assert row_data['readCount'] == 232
assert row_data['meanCoverage'] == 25.4946
assert row_data['sampleName'] == 'ADM992A10'
def test_expand_row_with_threshold():
header = {'extraFields': slice(3, 3), 'readCount': 3, 'meanCoverage': 4,
'thresholds': {10: 5, 20: 6, 100: 7}, 'sampleName': 8}
row = BASE_COLS + SAMBAMBA_COLS + THRESHOLD_COLS + SAMBAMBA_END_COLS
row_data = sambamba.expand_row(header, row)
assert row_data['thresholds'][10] == 57.9521
assert row_data['thresholds'][20] == 36.0566
assert row_data['thresholds'][100] == 5.55556
assert row_data['sampleName'] == 'ADM992A10'
def test_expand_row_basic():
header = {"extraFields": slice(3, 3), "readCount": 3, "meanCoverage": 4, "thresholds": {}, "sampleName": 5}
row = BASE_COLS + SAMBAMBA_COLS + SAMBAMBA_END_COLS
row_data = sambamba.expand_row(header, row)
assert row_data["chrom"] == "1"
assert row_data["chromStart"] == 69089
assert row_data["chromEnd"] == 70007
assert row_data["extraFields"] == []
assert row_data["readCount"] == 232
assert row_data["meanCoverage"] == 25.4946
assert row_data["thresholds"] == {}
assert row_data["sampleName"] == "ADM992A10"
def test_expand_row_basic():
header = {'extraFields': slice(3, 3), 'readCount': 3, 'meanCoverage': 4,
'thresholds': {}, 'sampleName': 5}
row = BASE_COLS + SAMBAMBA_COLS + SAMBAMBA_END_COLS
row_data = sambamba.expand_row(header, row)
assert row_data['chrom'] == '1'
assert row_data['chromStart'] == 69089
assert row_data['chromEnd'] == 70007
assert row_data['extraFields'] == []
assert row_data['readCount'] == 232
assert row_data['meanCoverage'] == 25.4946
assert row_data['thresholds'] == {}
assert row_data['sampleName'] == 'ADM992A10'
def test_expand_row_with_threshold():
header = {
"extraFields": slice(3, 3),
"readCount": 3,
"meanCoverage": 4,
"thresholds": {10: 5, 20: 6, 100: 7},
"sampleName": 8,
}
row = BASE_COLS + SAMBAMBA_COLS + THRESHOLD_COLS + SAMBAMBA_END_COLS
row_data = sambamba.expand_row(header, row)
assert row_data["thresholds"][10] == 57.9521
assert row_data["thresholds"][20] == 36.0566
assert row_data["thresholds"][100] == 5.55556
assert row_data["sampleName"] == "ADM992A10"
