From 6829496d44948608869ba8ed81ba5c060e970772 Mon Sep 17 00:00:00 2001
From: "Luis M. Rodriguez-R" <lmrodriguezr@gmail.com>
Date: Wed, 5 Jun 2024 20:34:22 +0200
Subject: [PATCH] Reduce "large" collection threshold in subclades

---
 lib/miga/version.rb | 2 +-
 utils/subclades.R   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/miga/version.rb b/lib/miga/version.rb
index e42c3e7..6282477 100644
--- a/lib/miga/version.rb
+++ b/lib/miga/version.rb
@@ -12,7 +12,7 @@ module MiGA
   # - String indicating release status:
   #   - rc* release candidate, not released as gem
   #   - [0-9]+ stable release, released as gem
-  VERSION = [1.3, 15, 5].freeze
+  VERSION = [1.3, 15, 6].freeze
 
   ##
   # Nickname for the current major.minor version.
diff --git a/utils/subclades.R b/utils/subclades.R
index fad803b..14f533e 100755
--- a/utils/subclades.R
+++ b/utils/subclades.R
@@ -147,7 +147,7 @@ subclade_clustering <- function (out_base, thr, ani.d, dist_rds) {
 
   # Classify genomes
   say("Classify => k :", top.n, "| n :", length(labels(ani.d)))
-  is.large <- nn > 3e4
+  is.large <- nn > 1e4
   ani.cl <- pam(ani.d, top.n, variant = "faster", do.swap = !is.large)
   ani.types <- ani.cl$clustering
   ani.medoids <- ani.cl$medoids