Options and defaults clean up for mappability output

Author: EricR86

newmap/main.py

@@ -3,6 +3,7 @@
 import sys
 
 from newmap import generate_index, unique_counts, unique_counts_conversion
+from newmap.unique_counts_conversion import STDOUT_FILENAME
 
 # Will throw PackagfeNotFoundError if package is not installed
 __version__ = version("newmap")
@@ -168,14 +169,14 @@ def parse_subcommands():
     # Add (non-positional) arguments for single-read bed file output
     generate_mappability_parser.add_argument(
         "--single-read-bed-file", "-s",
-        help="Filename for single-read mappability BED file output. Use '-' "
-             "for standard output.")
+        help="Filename for single-read mappability BED file output. Use '{}' "
+             "for standard output.".format(STDOUT_FILENAME))
 
     # Add (non-positional) arguments for multi-read wiggle file output
     generate_mappability_parser.add_argument(
         "--multi-read-wig-file", "-m",
-        help="Filename for multi-read mappability WIG file output. Use '-' "
-             "for standard output.")
+        help="Filename for multi-read mappability WIG file output. Use '{}' "
+             "for standard output.".format(STDOUT_FILENAME))
 
     generate_mappability_parser.add_argument(
         "--verbose",

newmap/unique_counts_conversion.py

@@ -8,16 +8,14 @@
 import numpy.typing as npt
 
 
-DEFAULT_KMER_SIZE = 24
+STDOUT_FILENAME = "-"
 CHROMOSOME_FILENAME_DELIMITER = ".unique"
 
 # chr_name, start, end, k-mer length, value
 BED_FILE_LINE_FORMAT = "{}\t{}\t{}\tk{}\t{}\t.\n"
 WIG_FIXED_STEP_DECLARATION_FORMAT = \
     "fixedStep chrom={} start={} step=1 span=1\n"
 
-STDOUT_FILENAME = "-"
-
 
 def create_multiread_mappability_from_unique_file(
      unique_lengths_filename: Path,