Merge pull request #10 from raufs/raufs-patch-1

Update to v1.3.2

Author: raufs

bin/skder

@@ -98,7 +98,7 @@ def create_parser():
 	parser.add_argument('-f', '--aligned-fraction-cutoff', type=float, help="Aligned cutoff threshold for dereplication - only needed by\none genome [Default is 50.0].", required=False, default=50.0)
 	parser.add_argument('-a', '--max-af-distance-cutoff', type=float, help="Maximum difference for aligned fraction between a pair to\nautomatically disqualify the genome with a higher\nAF from being a representative [Default is 10.0].", required=False, default=10.0)
 	parser.add_argument('-tc', '--test-cutoffs', action='store_true', help="Assess clustering using various pre-selected cutoffs.", required=False, default=False)
-	parser.add_argument('-p', '--skani-triangle-parameters', help="Options for skani triangle. Note ANI and AF cutoffs\nare specified separately and the -E parameter is always\nrequested. [Default is \"-s X\", where X is\n10 below the ANI cutoff].", default="-s 90.0", required=False)
+	parser.add_argument('-p', '--skani-triangle-parameters', help="Options for skani triangle. Note ANI and AF cutoffs\nare specified separately and the -E parameter is always\nrequested. [Default is \"-s X\", where X is\n10 below the ANI cutoff].", default="-s X", required=False)
 	parser.add_argument('-s', '--sanity-check', action='store_true', help="Confirm each FASTA file provided or downloaded is actually\na FASTA file. Makes it slower, but generally\ngood practice.", required=False, default=False)
 	parser.add_argument('-fm', '--filter-mge', action='store_true', help="Filter predicted MGE coordinates along genomes before\ndereplication assessment but after N50\ncomputation.", required=False, default=False)
 	parser.add_argument('-gd', '--genomad-database', help="If filter-mge is specified, it will by default use PhiSpy;\nhowever, if a database directory for\ngeNomad is provided - it will use that instead\nto predict MGEs.", default=None, required=False)

pyproject.toml

@@ -1,7 +1,7 @@
 [project]
 name = "skDER"
 authors = [{name="Rauf Salamzade", email="salamzader@gmail.com"}]
-version = "1.3.1"
+version = "1.3.2"
 description = "Program to select distinct representatives from an input set of microbial genomes."
 
 [build-system]