miga-base 1.2.1.0 → 1.2.2.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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+  metadata.gz: ab62d2e6d20aa126a5f455bd3b8159549d5c39b7b2e747587a0b0444a30d935a
+  data.tar.gz: 273671304affb6a21d1e4dc0374c4ff17edf39a96cba8893d2a666640ab1c7c9
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+  data.tar.gz: 1a7b42d7dc75c5cac04f3408e6fba0e989d46ac63e926602c020e15340e24e8dc4694bf07b5f75ecc3a707db9d110d4a379841c426f7eb4a5670da5bcfa9642e

data/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 = [1.2, 1, 0].freeze
+  VERSION = [1.2, 2, 0].freeze
 
   ##
   # Nickname for the current major.minor version.

data/utils/distance/commands.rb

@@ -111,12 +111,17 @@ module MiGA::DistanceRunner::Commands
     return unless File.size?(f1)
 
     # Run FastANI
+    empty = true
     File.open(f2 = tmp_file, 'w') do |fh|
       targets.each do |target|
         target_asm = target&.result(:assembly)&.file_path(:largecontigs)
-        fh.puts target_asm if target_asm
+        if target_asm
+          fh.puts target_asm
+          empty = false
+        end
       end
     end
+    return if empty
     run_cmd <<~CMD
               fastANI -q "#{f1}" --rl "#{f2}" -t #{opts[:thr]} \
               -o "#{f3 = tmp_file}"

data/utils/distance/pipeline.rb

@@ -33,6 +33,10 @@ module MiGA::DistanceRunner::Pipeline
 
   # Builds a tree with all visited medoids from any classification level
   def build_medoids_tree(metric)
+    # TODO Reduce impact and bring back the medoids tree
+    $stderr.puts 'Bypassing medoids tree'
+    return
+
     $stderr.puts "Building medoids tree (metric = #{metric})"
     db = query_db(metric)
     return unless File.size? db

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.2.1.0
+  version: 1.2.2.0
 platform: ruby
 authors:
 - Luis M. Rodriguez-R