Increase similarity threshold for fast mode

metagenopolis · Jan 14, 2025 · 953cc29 · 953cc29
1 parent d75cc19
commit 953cc29
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Showing 2 changed files with 1 addition and 3 deletions.
diff --git a/meteor/counter.py b/meteor/counter.py
@@ -16,7 +16,6 @@
 import sys
 import pysam
 import lzma
-import pandas as pd
 from dataclasses import dataclass, field
 from tempfile import mkdtemp, mkstemp
 from pathlib import Path
@@ -38,7 +37,7 @@ class Counter(Session):
     DEFAULT_COUNTING_TYPE: ClassVar[str] = "smart_shared"
     NO_IDENTITY_THRESHOLD: ClassVar[float] = 0.0
     DEFAULT_IDENTITY_THRESHOLD_COMPLETE: ClassVar[float] = 0.95
-    DEFAULT_IDENTITY_THRESHOLD_TAXO: ClassVar[float] = 0.97
+    DEFAULT_IDENTITY_THRESHOLD_TAXO: ClassVar[float] = 0.98
 
     meteor: type[Component]
     counting_type: str

diff --git a/meteor/session.py b/meteor/session.py
@@ -30,7 +30,6 @@ class Component:
 
     MIN_BOWTIE2_VERSION: ClassVar[Version] = Version("2.3.5")
     MIN_FREEBAYES_VERSION: ClassVar[Version] = Version("1.3.6")
-    # MIN_MAFFT_VERSION: ClassVar[Version] = Version("7.487")
     DEFAULT_GAP_CHAR: ClassVar[str] = "N"
     DEFAULT_CORE_SIZE: ClassVar[int] = 100