coutinho_assembly 0.2.1 → 0.3.0

checksums.yaml

@@ -1,7 +1,7 @@
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data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    coutinho_assembly (0.2.1)
+    coutinho_assembly (0.3.0)
 
 GEM
   remote: https://rubygems.org/

data/exe/coutinho_assembly

@@ -33,6 +33,8 @@ opts = Optimist.options do
 
   --sampling-percentage and --num-subsamples go together.  So, --sampling-percentage 1 5 10 --num-subsamples 50 35 25 would mean 50 1% subsamples, 35 5% subsamples, and 25 10% subsamples.
 
+  --megahit-presets See the megahit --help file for more information about these.  The "new" ones are fast which uses only kmer 21 assembly, and default, which uses whatever megahit has for the defaults.
+
   For the binary program options, either provide the path to the binary or the name of the program if the program is already on your path.
 
   Options:
@@ -79,8 +81,8 @@ opts = Optimist.options do
 
   # Megahit options
   opt(:megahit_presets,
-      "meta-sensitive, meta-large, or fast",
-      default: "meta-sensitive")
+      "meta-sensitive, meta-large, fast, or default",
+      default: "default")
 
   # External programs I depend on
   opt(:megahit_binary,
@@ -143,7 +145,7 @@ Rya::AbortIf.abort_if num_threads < 1,
 Rya::AbortIf.abort_if max_attempts < 1,
                       "--max-attempts must be at least 1"
 
-GOOD_PRESETS = %w[meta-sensitive meta-large fast]
+GOOD_PRESETS = %w[meta-sensitive meta-large fast default]
 megahit_preset = opts[:megahit_presets]
 Rya::AbortIf.abort_unless megahit_preset.nil? || GOOD_PRESETS.include?(megahit_preset),
                           "--megahit-presets must be one of #{GOOD_PRESETS.join(", ")}.  Got #{megahit_preset}"

data/lib/coutinho_assembly.rb

@@ -56,6 +56,7 @@ module CoutinhoAssembly
           cmd += " --out-prefix #{out_prefix}"
         end
 
+        # For preset of 'default' or anything else, just use the megahit default.
         if preset == "meta-sensitive"
           cmd += " --presets meta-sensitive"
         elsif preset == "meta-large"

data/lib/coutinho_assembly/version.rb

@@ -1,5 +1,5 @@
 module CoutinhoAssembly
-  VERSION = "0.2.1"
+  VERSION = "0.3.0"
 
   COPYRIGHT = "2019 Ryan Moore"
   CONTACT   = "moorer@udel.edu"

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: coutinho_assembly
 version: !ruby/object:Gem::Version
-  version: 0.2.1
+  version: 0.3.0
 platform: ruby
 authors:
 - Ryan Moore
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2019-04-15 00:00:00.000000000 Z
+date: 2019-04-30 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler