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"