Add cut_ga option and bump version to 0.10.3

cli/deciphon/cli.py

@@ -37,6 +37,9 @@
 O_HMMER3_COMPAT = Option(
     False, "--hmmer3-compat/--no-hmmer3-compat", help="Set hmmer3 compatibility."
 )
+O_CUT_GA = Option(
+    True, "--cut-ga/--no-cut-ga", help="Enable profile's GA gathering cutoffs."
+)
 H_HMMER = "HMMER profile file."
 
 
@@ -114,6 +117,7 @@ def scan(
     multi_hits: bool = O_MULTI_HITS,
     hmmer3_compat: bool = O_HMMER3_COMPAT,
     progress: bool = O_PROGRESS,
+    cut_ga: bool = O_CUT_GA,
 ):
     """
     Scan nucleotide sequences against protein database.
@@ -125,7 +129,7 @@ def scan(
 
         sequences = read_sequences(seqfile)
         with H3Daemon(hmm, stdout=DEVNULL) as daemon:
-            params = Params(num_threads, multi_hits, hmmer3_compat)
+            params = Params(num_threads, multi_hits, hmmer3_compat, cut_ga)
             scan = Scan(params, db)
             with scan:
                 bar = Progress(scan, disabled=not progress)

cli/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "deciphon"
-version = "0.10.2"
+version = "0.10.3"
 description = "Individually annotate long, error-prone nucleotide sequences into proteins"
 authors = ["Danilo Horta <[email protected]>"]
 license = "MIT"
@@ -10,7 +10,7 @@ packages = [{ include = "deciphon" }]
 [tool.poetry.dependencies]
 python = "^3.9"
 cffi = "^1.15.1"
-deciphon-core = ">=0.18.5"
+deciphon-core = ">=0.18.13"
 deciphon-snap = ">=0.8.1"
 fasta-reader = "^3"
 h3daemon = "^0"