from ALLCools.api import extract_allc
from .utilities import *


def test_extract_allc():
    for output_format in ["allc", "bed5"]:
        for strandness in ["both", "split", "merge"]:
            for cpu in [1, 4]:
                extract_allc(
                    allc_path=data_file_path("Cell01.allc.tsv.gz"),
                    output_prefix=output_path(
                        f"Cell01.allc.extract.{output_format}_{strandness}_cpu{cpu}"
                    ),
                    mc_contexts=["CHN", "CGN"],
                    chrom_size_path=CHROM_SIZE_PATH,
                    strandness=strandness,
                    output_format=output_format,
                    region=None,
                    cov_cutoff=9999,
                    tabix=True,
                    cpu=cpu,
                )
