fix some code (#17)

Author: ctb

pyproject.toml

@@ -3,7 +3,7 @@ name = "sourmash_plugin_pangenomics"
 description = "sourmash plugin to do pangenomics."
 readme = "README.md"
 requires-python = ">=3.10"
-version = "0.2.1"
+version = "0.2.2"
 authors = [
   {name = "Colton Baumler", email = "ccbaumler@ucdavis.edu"},
   {name = "Titus Brown", email = "titus@idyll.org"},

src/sourmash_plugin_pangenomics.py

@@ -145,7 +145,7 @@ def __init__(self, subparser):
         p.add_argument(
             "-o",
             "--output-hash-classification",
-            required=False,
+            required=True,
             help="CSV file containing classification of each hash",
         )
         sourmash_utils.add_standard_minhash_args(p)
@@ -447,15 +447,15 @@ def search_pattern(vals):
 
         for n, ss in enumerate(db.signatures()):
             if n % 10 == 0:
-                print(f"...Processing {n} of {len(mf)}", end="\r", flush=True)
+                print(f"...Processing {n} of {len(db)}", end="\r", flush=True)
 
                 name = ss.name
 
                 mh = ss.minhash
                 hashes = mh.hashes
                 ss_dict[name] = hashes
 
-            print(f"...Processed {n} of {len(mf)} \n")
+            print(f"...Processed {n+1} of {len(db)} \n")
 
     return ss_dict