Remove used parameter

meteor/counter.py

@@ -79,7 +79,6 @@ def launch_mapping(self) -> None:
                 self.mapping_type,
                 self.trim,
                 self.alignment_number,
-                self.counting_type,
                 self.identity_threshold,
             )
             mapping_process.execute()

meteor/mapper.py

@@ -45,7 +45,6 @@ class Mapper(Session):
     mapping_type: str
     trim: int
     alignment_number: int
-    counting_type: str
     identity_threshold: float
 
     def __post_init__(self) -> None:
@@ -117,7 +116,6 @@ def execute(self) -> None:
         if self.trim > Mapper.NO_TRIM:
             parameters += f"--trim-to {self.trim} "
         if self.alignment_number > 1:
-            # and self.counting_type != "best"
             parameters += f"-k {self.alignment_number} "
         # Check the bowtie2 version
         bowtie_exec = run(["bowtie2", "--version"], capture_output=True)

meteor/tests/test_mapper.py

@@ -52,7 +52,6 @@ def mapping_builder(datadir: Path, tmp_path: Path) -> Mapper:
         "end-to-end",
         80,
         10000,
-        "smart_shared_reads",
         0.95,
     )