finishm 0.0.7 → 0.0.8

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 97ecc9ab04ccb6e227d33d59a4219edfc0ba4614
-  data.tar.gz: 931671e63b1b82f20337dac7af39970d87f4c25a
+  metadata.gz: 00329e5c4f1171c274182bf82bfb5680eec1a488
+  data.tar.gz: 56995a8d5c0f1730aacbdc0f091ed38339fddba4
 SHA512:
-  metadata.gz: 48492828900c54d3fcbfd2e4ffae365476861a0cada3ed5b3c31917e9bc7bfc47a06055b1f1891003fad2896c5ce8b6576602a3c5e93c2ffab865001f3126065
-  data.tar.gz: 08d57f83a950941b8d202df5df572ee9735ba61a842e55d2c494169d24a248e7930c7034128981a1f8a09e4e09c17c161b6a662d5aa3090b09fc39720892dfe2
+  metadata.gz: fcfa56d35627cf62f66c57255231514b3dc24ab22907722098417a6c9a43a038ba36de68104f821b4dccc144cc5f59195a017494fd396da3026241b2c52b6fe9
+  data.tar.gz: 36ca079df399fb3bfacb2ae436fc3fda5ab755c7555e74cf5ce19a3be477e2d10d0d3d7f4f810fec6d9141bd431f50651e2469de43752e4fe495de8cb1a4e84f

data/Gemfile

@@ -6,7 +6,7 @@ gem 'bio-ipcress', '~>0.0'
 gem 'bio-logger', '~>1.0'
 gem 'bio', '~>1.4', '>=1.4.3'
 gem 'progressbar', '~>0.21'
-gem 'bio-samtools', '~>0.6'
+#gem 'bio-samtools', '~>2.4' # removed because even the newest version does not compile due to lacking zlib.h
 gem 'ruby-graphviz', '~>1.0', '>=1.0.9'
 gem 'ds', '~>0.0', '>=0.0.4'
 gem 'hopcsv', '~> 0.4', '>=0.4.3'
@@ -26,6 +26,6 @@ group :development do
   gem "yard", "~>0.7"
   gem "rdoc", "~>3.12"
   gem "bundler", "~>1.6", '>=1.6.2'
-  gem 'jeweler', '~>2.0', '>=2.0.1'
+  gem 'jeweler', '~>2.0', '>=2.1.1'
   gem 'bio-commandeer', '~>0.1'
 end

data/Rakefile

@@ -16,7 +16,7 @@ Jeweler::Tasks.new do |gem|
   # gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
   gem.name = "finishm"
   gem.homepage = "http://github.com/wwood/finishm"
-  gem.license = "GPL"
+  gem.license = "GPL3+"
   gem.summary = %Q{Genome improvement and finishing with or without further sequencing effort}
   gem.description = %Q{De-novo assemblies generally only provide draft genomes. FinishM is aimed at improving these draft assemblies.}
   gem.email = "donttrustben near gmail.com"

data/VERSION

@@ -1 +1 @@
-0.0.7
+0.0.8

data/finishm.gemspec

@@ -2,17 +2,17 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: finishm 0.0.7 ruby lib
+# stub: finishm 0.0.8 ruby lib
 # stub: ext/mkrf_conf.rb
 
 Gem::Specification.new do |s|
   s.name = "finishm"
-  s.version = "0.0.7"
+  s.version = "0.0.8"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.require_paths = ["lib"]
   s.authors = ["Ben J. Woodcroft"]
-  s.date = "2015-09-07"
+  s.date = "2016-08-01"
   s.description = "De-novo assemblies generally only provide draft genomes. FinishM is aimed at improving these draft assemblies."
   s.email = "donttrustben near gmail.com"
   s.executables = ["finishm"]
@@ -558,8 +558,8 @@ Gem::Specification.new do |s|
     "validation/gapfill_simulate_perfect.rb"
   ]
   s.homepage = "http://github.com/wwood/finishm"
-  s.licenses = ["GPL"]
-  s.rubygems_version = "2.2.2"
+  s.licenses = ["GPL3+"]
+  s.rubygems_version = "2.5.1"
   s.summary = "Genome improvement and finishing with or without further sequencing effort"
 
   if s.respond_to? :specification_version then
@@ -570,7 +570,6 @@ Gem::Specification.new do |s|
       s.add_runtime_dependency(%q<bio-logger>, ["~> 1.0"])
       s.add_runtime_dependency(%q<bio>, [">= 1.4.3", "~> 1.4"])
       s.add_runtime_dependency(%q<progressbar>, ["~> 0.21"])
-      s.add_runtime_dependency(%q<bio-samtools>, ["~> 0.6"])
       s.add_runtime_dependency(%q<ruby-graphviz>, [">= 1.0.9", "~> 1.0"])
       s.add_runtime_dependency(%q<ds>, [">= 0.0.4", "~> 0.0"])
       s.add_runtime_dependency(%q<hopcsv>, [">= 0.4.3", "~> 0.4"])
@@ -583,14 +582,13 @@ Gem::Specification.new do |s|
       s.add_development_dependency(%q<yard>, ["~> 0.7"])
       s.add_development_dependency(%q<rdoc>, ["~> 3.12"])
       s.add_development_dependency(%q<bundler>, [">= 1.6.2", "~> 1.6"])
-      s.add_development_dependency(%q<jeweler>, [">= 2.0.1", "~> 2.0"])
+      s.add_development_dependency(%q<jeweler>, [">= 2.1.1", "~> 2.0"])
       s.add_development_dependency(%q<bio-commandeer>, ["~> 0.1"])
     else
       s.add_dependency(%q<bio-ipcress>, ["~> 0.0"])
       s.add_dependency(%q<bio-logger>, ["~> 1.0"])
       s.add_dependency(%q<bio>, [">= 1.4.3", "~> 1.4"])
       s.add_dependency(%q<progressbar>, ["~> 0.21"])
-      s.add_dependency(%q<bio-samtools>, ["~> 0.6"])
       s.add_dependency(%q<ruby-graphviz>, [">= 1.0.9", "~> 1.0"])
       s.add_dependency(%q<ds>, [">= 0.0.4", "~> 0.0"])
       s.add_dependency(%q<hopcsv>, [">= 0.4.3", "~> 0.4"])
@@ -603,7 +601,7 @@ Gem::Specification.new do |s|
       s.add_dependency(%q<yard>, ["~> 0.7"])
       s.add_dependency(%q<rdoc>, ["~> 3.12"])
       s.add_dependency(%q<bundler>, [">= 1.6.2", "~> 1.6"])
-      s.add_dependency(%q<jeweler>, [">= 2.0.1", "~> 2.0"])
+      s.add_dependency(%q<jeweler>, [">= 2.1.1", "~> 2.0"])
       s.add_dependency(%q<bio-commandeer>, ["~> 0.1"])
     end
   else
@@ -611,7 +609,6 @@ Gem::Specification.new do |s|
     s.add_dependency(%q<bio-logger>, ["~> 1.0"])
     s.add_dependency(%q<bio>, [">= 1.4.3", "~> 1.4"])
     s.add_dependency(%q<progressbar>, ["~> 0.21"])
-    s.add_dependency(%q<bio-samtools>, ["~> 0.6"])
     s.add_dependency(%q<ruby-graphviz>, [">= 1.0.9", "~> 1.0"])
     s.add_dependency(%q<ds>, [">= 0.0.4", "~> 0.0"])
     s.add_dependency(%q<hopcsv>, [">= 0.4.3", "~> 0.4"])
@@ -624,7 +621,7 @@ Gem::Specification.new do |s|
     s.add_dependency(%q<yard>, ["~> 0.7"])
     s.add_dependency(%q<rdoc>, ["~> 3.12"])
     s.add_dependency(%q<bundler>, [">= 1.6.2", "~> 1.6"])
-    s.add_dependency(%q<jeweler>, [">= 2.0.1", "~> 2.0"])
+    s.add_dependency(%q<jeweler>, [">= 2.1.1", "~> 2.0"])
     s.add_dependency(%q<bio-commandeer>, ["~> 0.1"])
   end
 end

data/spec/data/explore/1/seq2.fa

@@ -0,0 +1 @@
+../../fluff/1/seq2.fa

data/spec/data/gapfilling/3/reference_part1.fa

@@ -0,0 +1 @@
+../2/reference_part1.fa

data/spec/data/gapfilling/3/reference_part2.fa

@@ -0,0 +1 @@
+../2/reference_part2.fa

data/spec/data/gapfilling/3/with_gaps.fa

@@ -0,0 +1 @@
+../2/with_gaps.fa

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: finishm
 version: !ruby/object:Gem::Version
-  version: 0.0.7
+  version: 0.0.8
 platform: ruby
 authors:
 - Ben J. Woodcroft
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-09-07 00:00:00.000000000 Z
+date: 2016-08-01 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio-ipcress
@@ -72,20 +72,6 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '0.21'
-- !ruby/object:Gem::Dependency
-  name: bio-samtools
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '0.6'
-  type: :runtime
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '0.6'
 - !ruby/object:Gem::Dependency
   name: ruby-graphviz
   requirement: !ruby/object:Gem::Requirement
@@ -302,7 +288,7 @@ dependencies:
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 2.0.1
+        version: 2.1.1
     - - "~>"
       - !ruby/object:Gem::Version
         version: '2.0'
@@ -312,7 +298,7 @@ dependencies:
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 2.0.1
+        version: 2.1.1
     - - "~>"
       - !ruby/object:Gem::Version
         version: '2.0'
@@ -877,7 +863,7 @@ files:
 - validation/gapfill_simulate_perfect.rb
 homepage: http://github.com/wwood/finishm
 licenses:
-- GPL
+- GPL3+
 metadata: {}
 post_install_message: 
 rdoc_options: []
@@ -895,7 +881,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.2.2
+rubygems_version: 2.5.1
 signing_key: 
 specification_version: 4
 summary: Genome improvement and finishing with or without further sequencing effort

data/spec/data/explore/1/seq2.fa

@@ -1,2 +0,0 @@
->1111886
-AACGAACGCTGGCGGCATGCCTAACACATGCAAGTCGAACGAGACCTTCGGGTCTAGTGGCGCACGGGTGCGTAACGCGTGGGAATCTGCCCTTGGGTACGGAATAACAGTTAGAAATGACTGCTAATACCGTATAATGACTTCGGTCCAAAGATTTATCGCCCAGGGATGAGCCCGCGTAGGATTAGCTTGTTGGTGAGGTAAAGGCTCACCAAGGCGACGATCCTTAGCTGGTCTGAGAGGATGATCAGCCACACTGGGACTGAGACATGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCAATGCCGCGTGAGTGATGAAGGCCTTAGGGTTGTAAAGCTCTTTTACCCGGGATGATAATGACAGTACCGGGAGAATAAGCCCCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGGGCTAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGTAGGCGGCTTTGTAAGTTAGAGGTGAAAGCCCGGGGCTCAACTCCGGAATTGCCTTTAAGACTGCATCGCTAGAATTGTGGAGAGGTGAGTGGAATTCCGAGTGTAGAGGTGAAATTCGTAGATATTCGGAAGAACACCAGTGGCGAAGGCGACTCACTGGACACATATTGACGCTGAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGATGACTAGCTGTCGGGGCGCTTAGCGTTTCGGTGGCGCAGCTAACGCGTTAAGTCATCCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAAGAAATTGACGGGGGCCTGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGCAGAACCTTACCAGCGTTTGACATGGTAGGACGGTTTCCAGAGATGGATTCCTACCCTTACGGGACCTACACACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTCGTCTTTGGTTGCTACCATTTAGTTGAGCACTCTAAAAAAACTGCCGGTGATAAGCCGGAGGAAGGTGGGGATGACGTCAAGTCCTCATAGCCCTTACGCGCTGGGCTACACACGTGCTACAATGGCGGTGACAGAGGGCAGCAAACCCGCGAGGGTGAGCTAATCTCCAAAAGCCGTCTCAGTTCGGATTGTTCTCTGCAACTCGAGAGCATGAAGGCGGAATCGCTAGTAATCGCGGATCAGCACGCCGCGGTGAATACGTTCCCAGGCCTTGTACACACCGCCCGTCACATCACGAAAGTCGGTTGCACTAGAAGTCGGTGGGCTAACCCGCAAGGGAGGCAGCCGCCTAAAGTGTGATCGGTAATTGGGGTG

data/spec/data/gapfilling/3/reference_part1.fa

@@ -1,4 +0,0 @@
->1111883_chopped_1-1000
-GCTGGCGGCGTGCCTAACACATGTAAGTCGAACGGGACTGGGGGCAACTCCAGTTCAGTGGCAGACGGGTGCGTAACACGTGAGCAACTTGTCCGACGGCGGGGGATAGCCGGCCCAACGGCCGGGTAATACCGCGTACGCTCGTTTAGGGACATCCCTGAATGAGGAAAGCCGTAAGGCACCGACGGAGAGGCTCGCGGCCTATCAGCTAGTTGGCGGGGTAACGGCCCACCAAGGCGACGACGGGTAGCTGGTCTGAGAGGATGGCCAGCCACATTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATCTTGCGCAATGGCCGCAAGGCTGACGCAGCGACGCCGCGTGTGGGATGACGGCCTTCGGGTTGTAAACCACTGTCGGGAGGAACGAATACTCGGCTAGTCCGAGGGTGACGGTACCTCCAAAGGAAGCACCGGCTAACTCC
-GTGCCAGCAGCCGCGGTAATACGGAGGGTGCGAGCGTTGTCCGGAATCACTGGGCGTAA
-AGGGCGCGTAGGTGGCCCGTTAAGTGGCTGGTGAAATCCCGGGGCTCAACTCCGGGGCTGCCGGTCAGACTGGCGAGCTAGAGCACGGTAGGGGCAGATGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAAGAATACCAGTGGCGAAGGCGTTCTGCTGGGCCGTTGCTGACACTGAGGCGCGACAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGGACACTAGACGTCGGGGGGAGCGACCCTCCCGGTGTCGTCGCTAACGCAGTAAGTGTCCCGCCTGGGGAGTACGGCCGCAAGGCTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAACCTTACCTGGGCTTGACATGCTGGTGCAAGCCGGTGGAAACATCGGCCCCTCTTCGGAGCGCCAGCAC

data/spec/data/gapfilling/3/reference_part2.fa

@@ -1,4 +0,0 @@
->1111883_chopped_1-1000_with_1000to1100_insertion
-GCTGGCGGCGTGCCTAACACATGTAAGTCGAACGGGACTGGGGGCAACTCCAGTTCAGTGGCAGACGGGTGCGTAACACGTGAGCAACTTGTCCGACGGCGGGGGATAGCCGGCCCAACGGCCGGGTAATACCGCGTACGCTCGTTTAGGGACATCCCTGAATGAGGAAAGCCGTAAGGCACCGACGGAGAGGCTCGCGGCCTATCAGCTAGTTGGCGGGGTAACGGCCCACCAAGGCGACGACGGGTAGCTGGTCTGAGAGGATGGCCAGCCACATTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATCTTGCGCAATGGCCGCAAGGCTGACGCAGCGACGCCGCGTGTGGGATGACGGCCTTCGGGTTGTAAACCACTGTCGGGAGGAACGAATACTCGGCTAGTCCGAGGGTGACGGTACCTCCAAAGGAAGCACCGGCTAACTCC
-CAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACTCTCGCTCCCAGTTGCCAGCGGTTCGGCCGGGG
-AGGGCGCGTAGGTGGCCCGTTAAGTGGCTGGTGAAATCCCGGGGCTCAACTCCGGGGCTGCCGGTCAGACTGGCGAGCTAGAGCACGGTAGGGGCAGATGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAAGAATACCAGTGGCGAAGGCGTTCTGCTGGGCCGTTGCTGACACTGAGGCGCGACAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGGACACTAGACGTCGGGGGGAGCGACCCTCCCGGTGTCGTCGCTAACGCAGTAAGTGTCCCGCCTGGGGAGTACGGCCGCAAGGCTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAACCTTACCTGGGCTTGACATGCTGGTGCAAGCCGGTGGAAACATCGGCCCCTCTTCGGAGCGCCAGCAC

data/spec/data/gapfilling/3/with_gaps.fa

@@ -1,4 +0,0 @@
->1111883_chopped_1-1000_with_some_gap_characters
-GCTGGCGGCGTGCCTAACACATGTAAGTCGAACGGGACTGGGGGCAACTCCAGTTCAGTGGCAGACGGGTGCGTAACACGTGAGCAACTTGTCCGACGGCGGGGGATAGCCGGCCCAACGGCCGGGTAATACCGCGTACGCTCGTTTAGGGACATCCCTGAATGAGGAAAGCCGTAAGGCACCGACGGAGAGGCTCGCGGCCTATCAGCTAGTTGGCGGGGTAACGGCCCACCAAGGCGACGACGGGTAGCTGGTCTGAGAGGATGGCCAGCCACATTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATCTTGCGCAATGGCCGCAAGGCTGACGCAGCGACGCCGCGTGTGGGATGACGGCCTTCGGGTTGTAAACCACTGTCGGGAGGAACGAATACTCGGCTAGTCCGAGGGTGACGGTACCTCCAAAGGAAGCACCGGCTAACTCC
-NNNNNNNNNNNNNNNNN
-AGGGCGCGTAGGTGGCCCGTTAAGTGGCTGGTGAAATCCCGGGGCTCAACTCCGGGGCTGCCGGTCAGACTGGCGAGCTAGAGCACGGTAGGGGCAGATGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAAGAATACCAGTGGCGAAGGCGTTCTGCTGGGCCGTTGCTGACACTGAGGCGCGACAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGGACACTAGACGTCGGGGGGAGCGACCCTCCCGGTGTCGTCGCTAACGCAGTAAGTGTCCCGCCTGGGGAGTACGGCCGCAAGGCTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAACCTTACCTGGGCTTGACATGCTGGTGCAAGCCGGTGGAAACATCGGCCCCTCTTCGGAGCGCCAGCAC