Add support from writing bigWig files with pybigtools instead of pyBi…

…gWig.

Add support from writing bigWig files with pybigtools instead of pyBigWig.

src/scatac_fragment_tools/cli/commands.py

@@ -40,7 +40,8 @@ def command_fragment_to_bigwigs(args):
         args.normalize,
         args.scaling_factor,
         args.cut_sites,
-        args.verbose
+        args.bigwig_writer,
+        args.verbose,
     )
 
 def command_split_fragments_by_cell_type(args):

src/scatac_fragment_tools/cli/main.py

@@ -18,6 +18,7 @@
 _OPTIONAL_ARGUMENTS_NAME = "Optional arguments"
 _FORMATTER_CLASS = RichHelpFormatter
 
+
 class SubparserBuilder:
     """
     Helper class for building subparsers.
@@ -118,6 +119,16 @@ def add_fragments_to_bigwig_subparser(
         help="Use 1 bp Tn5 cut sites (start and end of each fragment) instead of whole "
         "fragment length for coverage calculation.",
     )
+    parser.add_optional_argument(
+        "-w",
+        "--writer",
+        dest="bigwig_writer",
+        action="store",
+        type=str.lower,
+        choices=["pybigtools", "pybigwig"],
+        default="pybigwig",
+        help="Which bigWig writer implementation to use.",
+    )
     parser.add_optional_argument(
         "--chrom-prefix",
         dest="chrom_prefix",