diff --git a/cooltools/api/coverage.py b/cooltools/api/coverage.py index 6b8342a3..1b298e37 100644 --- a/cooltools/api/coverage.py +++ b/cooltools/api/coverage.py @@ -63,7 +63,7 @@ def _get_chunk_coverage(chunk, pixel_weight_key="count"): def coverage( clr, - ignore_diags=None, + ignore_diags="auto", chunksize=int(1e7), map=map, use_lock=False, @@ -95,7 +95,7 @@ def coverage( ignore_diags : int, optional Drop elements occurring on the first ``ignore_diags`` diagonals of the matrix (including the main diagonal). - If None, equals the number of diagonals ignored during IC balancing. + If auto, equals the number of diagonals ignored during IC balancing. store : bool, optional If True, store the results in the input cooler file when finished. If clr_weight_name=None, also stores total cis counts in the cooler info. Default is False. @@ -113,7 +113,7 @@ def coverage( try: ignore_diags = ( ignore_diags - if ignore_diags is not None + if ignore_diags != "auto" else clr._load_attrs(clr.root.rstrip("/") + "/bins/weight")["ignore_diags"] ) except: diff --git a/cooltools/cli/coverage.py b/cooltools/cli/coverage.py index 98d82fdb..8e46a6ca 100644 --- a/cooltools/cli/coverage.py +++ b/cooltools/cli/coverage.py @@ -25,8 +25,6 @@ help="The number of diagonals to ignore. By default, equals" " the number of diagonals ignored during IC balancing.", type=int, - default=None, - show_default=True, ) @click.option( "--store",