Commit 04ebab2b authored by MARIJON Pierre's avatar MARIJON Pierre

Add test where an overlap diseapear because it's iternal match

parent 40008720
import pytest
import logging
import paf2gfa
def test_overlap_poped():
paf = """
57569 26221 1475 20050 - 60137 26950 8 18545 2156 18575 255 cm:i:258
57569 26221 195 18981 - 58292 33025 73 18781 1881 18786 255 cm:i:210
57569 26221 8737 25698 + 59880 37403 338 17320 1878 16982 255 cm:i:209
58292 33025 79 25731 + 60137 26950 1097 26798 2715 25701 255 cm:i:295
58292 33025 8282 32847 - 58572 32242 7553 32158 2364 24605 255 cm:i:260
58292 33025 83 10607 - 59880 37403 35 10589 985 10554 255 cm:i:102
58292 33025 26451 32902 + 60730 26036 56 6495 526 6451 255 cm:i:58
59880 37403 10 11577 - 60137 26950 109 11633 1100 11567 255 cm:i:122
"""
true = """
"""
all_ov = paf2gfa.Parser()
selected_ov = paf2gfa.Parser(False, False)
all_ov.parse_lines(paf.split("\n"))
selected_ov.parse_lines(paf.split("\n"))
all_ov.clean_data()
all_ov.clean_data()
assert set(all_ov.get_gfa().strip().split("\n")) != set(selected_ov.get_gfa().strip().split("\n"))
def test_overlap_poped_short():
logger = logging.getLogger()
logger.setLevel(logging.DEBUG)
stream_handler = logging.StreamHandler()
stream_handler.setLevel(logging.DEBUG)
logger.addHandler(stream_handler)
paf = """
57569 26221 1475 20050 - 60137 26950 8 18545 2156 18575 255 cm:i:258
"""
true = """
"""
all_ov = paf2gfa.Parser()
selected_ov = paf2gfa.Parser(False, False)
all_ov.parse_lines(paf.split("\n"))
selected_ov.parse_lines(paf.split("\n"))
all_ov.clean_data()
all_ov.clean_data()
assert set(all_ov.get_gfa().strip().split("\n")) != set(selected_ov.get_gfa().strip().split("\n"))
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