miga-base 1.2.4.0 → 1.2.5.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 5a2b155a7dd169adddb5bc6c1470c252adb2357521e5df1cb37634a80031a123
-  data.tar.gz: dc99e9614989ea17bf173c8d1fc8c1f0dd5692030079d54197099471f8f17041
+  metadata.gz: e020ccd1d0a0291a8bc271432fe1dceccbe27c794295942bc6ad2e57ffcd9539
+  data.tar.gz: 7998b7647cefd9e09a06143f019acb01ee436e28e5f0f87aafbb677674b5cf62
 SHA512:
-  metadata.gz: e4d1271135ba5c66a712f6ba7f19e14b351b367342d0a6f8e268ede58f7d85cc5bc2c4830040cdfa0e9bb742075ef61de4bf0cd086e075e9318ba4cd62eba4e2
-  data.tar.gz: 95d6881e9c0df6f5d2dbbef6f0ae144ac922a1e1a3b355785f78376cef1ed1e8b783ea08bf24674b6e17ca5543d90cc4555b11f11c261baa574398ddace9bb97
+  metadata.gz: 3752e382431318bab43319ae6bb2a1725d5c66593a6bd144c8d6623219ab4ca5833764037cb8e59a8e491f44fb0cda8b4e001dd821ba0e6ca793ea7986c1f4e1
+  data.tar.gz: dea859f260cc498967d23190bc899c2a591577312b9208933b8750c4874a5a5664e4d1999e49b8152c6e7fc6cef02ab5e54825d9f5815e89cae39ff2775fcb84

data/lib/miga/cli/action/run.rb

@@ -59,7 +59,7 @@ class MiGA::Cli::Action::Run < MiGA::Cli::Action
     if cli[:check_first]
       obj = cli[:dataset] ? p.dataset(cli[:dataset]) : p
       if obj.result(cli[:result])
-        cli.say 'Result already exists'
+        cli.say('Result already exists')
         return
       end
     end

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, 4, 0].freeze
+  VERSION = [1.2, 5, 0].freeze
 
   ##
   # Nickname for the current major.minor version.
@@ -20,7 +20,7 @@ module MiGA
 
   ##
   # Date of the current gem relese.
-  VERSION_DATE = Date.new(2022, 2, 25)
+  VERSION_DATE = Date.new(2022, 5, 9)
 
   ##
   # References of MiGA

data/scripts/trimmed_fasta.bash

@@ -15,7 +15,7 @@ miga date > "$DATASET.start"
 for s in 1 2 ; do
   in="../02.trimmed_reads/${b}.${s}.clipped.fastq.gz"
   [[ -s "$in" ]] \
-    && FastQ.maskQual.rb -i "$in" -o "${b}.1.fasta" --fasta --qual 18
+    && FastQ.maskQual.rb -i "$in" -o "${b}.${s}.fasta" --fasta --qual 18
 done
 
 # Interpose

data/utils/distance/commands.rb

@@ -216,11 +216,12 @@ module MiGA::DistanceRunner::Commands
       next unless target_ess
 
       # hAAI
-      h = aairb_cmd(
-            tmp_file('ess_genes.fa'), target_ess,
-            dataset.name, target.name, tmp_dbs[:haai],
-            aai_save_rbm: false, aai_p: opts[:haai_p], checkpoint: :haai
-          )&.chomp&.to_f
+      aairb_cmd(
+        tmp_file('ess_genes.fa'), target_ess,
+        dataset.name, target.name, tmp_dbs[:haai],
+        aai_save_rbm: false, aai_p: opts[:haai_p], checkpoint: :haai
+      )
+      h = value_from_db(dataset.name, target.name, tmp_dbs[:haai], :haai)
       next if h.nil? || h.zero? || h > 90.0
 
       # Estimated AAI

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.2.4.0
+  version: 1.2.5.0
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2022-02-25 00:00:00.000000000 Z
+date: 2022-05-09 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons