transrate 1.0.0.beta5 → 1.0.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
checksums.yaml CHANGED
@@ -1,7 +1,7 @@
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+ metadata.gz: 1cdc0e54bd5a77cc14727d6c42e739e6c9fa4d10
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+ data.tar.gz: f55918c002f429f1d4912feca88b91e7647bb4064348e254860673d8d9d52bd8bad512b3f7e23e166ad87defbe67de51eeb043620a43dc51eed61e4d40aeece1
data/.gitignore CHANGED
@@ -67,3 +67,6 @@ traveling-ruby*
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  *box
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  libruby.so*
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  libruby*dylib
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+
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+ # example data
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+ example_data*
data/Rakefile CHANGED
@@ -90,7 +90,7 @@ task :default => :test
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  # PACKAGING
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  PACKAGE_NAME = "transrate"
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- VERSION = "1.0.0.beta4"
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+ VERSION = "1.0.0"
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  TRAVELING_RUBY_VERSION = "20150210-2.2.0"
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  desc "Package your app"
@@ -156,10 +156,11 @@ def create_package(target)
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  sh "mkdir packaging/bindeps/#{target}/{bin,lib}"
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  sh "cd packaging/bindeps/#{target} && " +
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  "find . -maxdepth 1 -name '*.tar.gz' -exec tar -xzf '{}' \\; && " +
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- "mv snap bam-read bin/"
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+ "mv snap-aligner bam-read bin/ && cp -r ./*/{bin,lib} ."
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  sh "cp -r packaging/bindeps/#{target}/{bin,lib} #{package_dir}/"
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  # install c extension
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- sh "cp test/vagrant/#{target}/{transrate,libruby}.* #{package_dir}/lib/"
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+ sh "cp test/vagrant/#{target}/libruby.* #{package_dir}/lib/"
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+ sh "cp test/vagrant/#{target}/transrate.* #{package_dir}/lib/app/ext/transrate/"
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  # create package
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  if !ENV['DIR_ONLY']
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  sh "cd packaging && tar -czf #{package_pref}.tar.gz #{package_pref}"
@@ -173,11 +173,11 @@ else
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  end
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  puts "To install all missing dependencies, run:"
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- puts " transrate --install-deps"
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+ puts " transrate --install-deps a;;"
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  puts "If you only want the read-metrics dependencies:"
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- puts " transrate --install-read-deps"
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+ puts " transrate --install-deps read"
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  puts "Or if you only want the reference-metrics dependencies: "
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- puts " transrate --install-ref-deps"
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+ puts " transrate --install-deps ref"
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  exit 1
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  end
@@ -290,7 +290,7 @@ assemblies.split(',').each do |assembly|
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  pretty_print_hash(contig_results, report_width)
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  end
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- logger.info "Contig metrics done in #{Time.now - t0} seconds"
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+ logger.info "Contig metrics done in #{(Time.now - t0).round} seconds"
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  read_results = {}
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@@ -305,7 +305,7 @@ assemblies.split(',').each do |assembly|
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  pretty_print_hash(read_results, report_width)
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  end
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- logger.info "Read metrics done in #{Time.now - t0} seconds"
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+ logger.info "Read metrics done in #{(Time.now - t0).round} seconds"
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  else
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  logger.info "No reads provided, skipping read diagnostics"
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  end
@@ -324,7 +324,7 @@ assemblies.split(',').each do |assembly|
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  pretty_print_hash(comparative_results, report_width)
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  end
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- logger.info "Comparative metrics done in #{Time.now - t0} seconds"
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+ logger.info "Comparative metrics done in #{(Time.now - t0).round} seconds"
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  logger.info "-" * report_width
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  else
@@ -366,7 +366,7 @@ assemblies.split(',').each do |assembly|
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  csv << basic_metrics.keys
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  first = false
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  end
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- csv << basic_metrics.values
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+ csv << basic_metrics.values.map{ |x| x.is_a?(Float) ? x.round(6) : x }
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  end
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  end
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@@ -388,6 +388,9 @@ CSV.open(outfile, 'wb') do |file|
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  head = [:assembly] + keys
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  file << head
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  all.each do |row|
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- file << head.map { |x| row[x] }
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+ file << head.map { |x|
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+ entry = row[x]
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+ entry.is_a?(Float) ? entry.round(5) : entry
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+ }
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  end
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  end
@@ -1,23 +1,23 @@
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  snap:
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  binaries:
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- - snap
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+ - snap-aligner
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  version:
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- number: '1.0dev.67.trfix1'
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- command: 'snap'
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+ number: '1.0beta.18'
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+ command: 'snap-aligner'
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  url:
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  64bit:
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- linux: https://github.com/Blahah/snap/releases/download/v1.0dev.67.trfix1/snap_v1.0dev.67.trfix1_linux.tar.gz
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- macosx: https://github.com/Blahah/snap/releases/download/v1.0dev.67.trfix1/snap_v1.0dev.67.trfix1_macosx.tar.gz
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+ linux: https://github.com/Blahah/snap/releases/download/v1.0beta.18/snap_v1.0beta.18_linux.tar.gz
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+ macosx: https://github.com/Blahah/snap/releases/download/v1.0beta.18/snap_v1.0beta.18_osx.tar.gz
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  bam-read:
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  binaries:
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  - bam-read
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  version:
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- number: '1.0.0.beta4'
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+ number: '1.0.0'
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  command: 'bam-read'
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  url:
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  64bit:
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- linux: https://github.com/Blahah/transrate-tools/releases/download/v1.0.0.beta4/bam-read_v1.0.0.beta4_linux.tar.gz
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- macosx: https://github.com/Blahah/transrate-tools/releases/download/v1.0.0.beta4/bam-read_v1.0.0.beta4_osx.tar.gz
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+ linux: https://github.com/Blahah/transrate-tools/releases/download/v1.0.0/bam-read_v1.0.0_linux.tar.gz
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+ macosx: https://github.com/Blahah/transrate-tools/releases/download/v1.0.0/bam-read_v1.0.0_osx.tar.gz
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  unpack: true
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  salmon:
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  binaries:
@@ -45,5 +45,5 @@ salmon:
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  command: 'salmon -v'
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  url:
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  64bit:
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- linux: https://github.com/COMBINE-lab/salmon/releases/download/v0.4.0/SalmonBeta-0.4.0_DebianSqueeze.tar.gz
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- macosx: https://github.com/COMBINE-lab/salmon/releases/download/v0.4.0/SalmonBeta-0.4.0_OSX-10.10.tar.gz
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+ linux: https://github.com/COMBINE-lab/salmon/releases/download/v0.4.2/SalmonBeta-0.4.2_DebianSqueeze.tar.gz
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+ macosx: https://github.com/COMBINE-lab/salmon/releases/download/v0.4.2/SalmonBeta-0.4.2_OSX-10.10.tar.gz
@@ -26,6 +26,7 @@ module Transrate
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  end # Transrate
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+ require 'transrate/transrate'
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  require 'transrate/transrater'
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  require 'transrate/version'
31
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  require 'transrate/contig'
@@ -49,7 +49,7 @@ module Transrate
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  out = CSV.open("#{prefix}_score_optimisation.csv", 'w')
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  out << %w[cutoff assembly_score]
51
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  cutoffscores.each do |c, score|
52
- out << [c, score]
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+ out << [c.round(5), score.round(5)]
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  if score > @optimal
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  @optimal = score
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  @cutoff = c
@@ -11,7 +11,7 @@ module Transrate
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  attr_reader :index_name, :bam, :read_count
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  def initialize
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- which_snap = Cmd.new('which snap')
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+ which_snap = Cmd.new('which snap-aligner')
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  which_snap.run
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  if !which_snap.status.success?
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  raise SnapError.new("could not find snap in the path")
@@ -11,7 +11,7 @@ module Transrate
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  MAJOR = 1
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  MINOR = 0
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  PATCH = 0
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- BUILD = 'beta5'
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+ BUILD = nil
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  STRING = [MAJOR, MINOR, PATCH, BUILD].compact.join('.')
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  end
@@ -8,13 +8,14 @@ SimpleCov.formatter = SimpleCov::Formatter::MultiFormatter[
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  SimpleCov.start
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  require 'minitest/autorun'
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- begin; require 'turn/autorun'; rescue LoadError; end
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+ begin
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+ require 'turn/autorun'
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+ Turn.config.format = :pretty
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+ Turn.config.trace = 5
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+ rescue LoadError
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+ end
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  require 'shoulda/context'
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  require 'transrate'
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- require 'transrate/transrate.so'
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-
16
- Turn.config.format = :pretty
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- Turn.config.trace = 5
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  # download large fastq files into test/data/.
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  path = "https://github.com/HibberdLab/transrate-test-files/raw/master"
@@ -27,4 +28,4 @@ test_files.each do |file|
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  cmd = Transrate::Cmd.new(wget_cmd)
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  cmd.run
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  end
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- end
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+ end
@@ -31,7 +31,7 @@ class TestReadMetrics < Test::Unit::TestCase
31
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  stats = @read_metrics.read_stats
32
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  assert @read_metrics.has_run, "has run"
33
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  assert_equal 25006, stats[:fragments], 'number of read pairs'
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- assert_in_delta 21744, stats[:fragments_mapped], 10, 'number mapping'
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+ assert_in_delta 21732, stats[:fragments_mapped], 10, 'number mapping'
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  assert_in_delta 0.84, stats[:p_fragments_mapped].round(4), 0.05
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  'proportion mapping'
37
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  assert_in_delta 17983, stats[:good_mappings], 50, 'good mapping'
@@ -61,7 +61,7 @@ class TestReadMetrics < Test::Unit::TestCase
61
61
 
62
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  edit_a = a[:p_seq_true].round(5)
63
63
  edit_b = b[:p_seq_true].round(5)
64
- assert_in_delta 0.6597, edit_a.round(4), 0.01, "edit distance 1"
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+ assert_in_delta 0.7086, edit_a.round(4), 0.01, "edit distance 1"
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65
  assert_in_delta 0.9364, edit_b.round(4), 0.01, "edit distance 2"
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  assert_in_delta 0.5714, a[:p_good].round(4), 0.01, "prop of good mappings"
@@ -4,7 +4,7 @@ require File.expand_path('../lib/transrate/version', __FILE__)
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5
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  Gem::Specification.new do |gem|
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  gem.name = 'transrate'
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- gem.authors = [ "Richard Smith-Unna", "Chris Boursnell" ]
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+ gem.authors = [ "Richard Smith-Unna", "Chris Boursnell", "Rob Patro", "Julian Hibberd", "Steven Kelly" ]
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  gem.email = "rds45@cam.ac.uk"
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  gem.licenses = ["MIT"]
10
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  gem.homepage = 'https://github.com/Blahah/transrate'
@@ -25,11 +25,12 @@ Gem::Specification.new do |gem|
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  gem.add_dependency 'fix-trinity-output', '~> 1.0', '>= 1.0'
26
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  gem.add_dependency 'colorize', '~> 0.7', '>= 0.7.7'
27
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28
+ gem.add_development_dependency 'test-unit', '~> 3.0'
28
29
  gem.add_development_dependency 'rake', '~> 10.3', '>= 10.3.2'
29
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  gem.add_development_dependency 'rake-compiler', '~> 0.9', '>= 0.9.2'
30
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  gem.add_development_dependency 'turn', '~> 0.9', '>= 0.9.7'
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  gem.add_development_dependency 'minitest', '~> 4', '>= 4.7.5'
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  gem.add_development_dependency 'simplecov', '~> 0.8', '>= 0.8.2'
33
- gem.add_development_dependency 'shoulda-context', '~> 1.2', '>= 1.2.1'
34
+ gem.add_development_dependency 'shoulda', '~> 3.5', '>= 3.5.0'
34
35
  gem.add_development_dependency 'coveralls', '~> 0.7', '>= 0.7.2'
35
36
  end
metadata CHANGED
@@ -1,15 +1,18 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: transrate
3
3
  version: !ruby/object:Gem::Version
4
- version: 1.0.0.beta5
4
+ version: 1.0.0
5
5
  platform: ruby
6
6
  authors:
7
7
  - Richard Smith-Unna
8
8
  - Chris Boursnell
9
+ - Rob Patro
10
+ - Julian Hibberd
11
+ - Steven Kelly
9
12
  autorequire:
10
13
  bindir: bin
11
14
  cert_chain: []
12
- date: 2015-06-11 00:00:00.000000000 Z
15
+ date: 2015-06-15 00:00:00.000000000 Z
13
16
  dependencies:
14
17
  - !ruby/object:Gem::Dependency
15
18
  name: yell
@@ -151,6 +154,20 @@ dependencies:
151
154
  - - ">="
152
155
  - !ruby/object:Gem::Version
153
156
  version: 0.7.7
157
+ - !ruby/object:Gem::Dependency
158
+ name: test-unit
159
+ requirement: !ruby/object:Gem::Requirement
160
+ requirements:
161
+ - - "~>"
162
+ - !ruby/object:Gem::Version
163
+ version: '3.0'
164
+ type: :development
165
+ prerelease: false
166
+ version_requirements: !ruby/object:Gem::Requirement
167
+ requirements:
168
+ - - "~>"
169
+ - !ruby/object:Gem::Version
170
+ version: '3.0'
154
171
  - !ruby/object:Gem::Dependency
155
172
  name: rake
156
173
  requirement: !ruby/object:Gem::Requirement
@@ -252,25 +269,25 @@ dependencies:
252
269
  - !ruby/object:Gem::Version
253
270
  version: 0.8.2
254
271
  - !ruby/object:Gem::Dependency
255
- name: shoulda-context
272
+ name: shoulda
256
273
  requirement: !ruby/object:Gem::Requirement
257
274
  requirements:
258
275
  - - "~>"
259
276
  - !ruby/object:Gem::Version
260
- version: '1.2'
277
+ version: '3.5'
261
278
  - - ">="
262
279
  - !ruby/object:Gem::Version
263
- version: 1.2.1
280
+ version: 3.5.0
264
281
  type: :development
265
282
  prerelease: false
266
283
  version_requirements: !ruby/object:Gem::Requirement
267
284
  requirements:
268
285
  - - "~>"
269
286
  - !ruby/object:Gem::Version
270
- version: '1.2'
287
+ version: '3.5'
271
288
  - - ">="
272
289
  - !ruby/object:Gem::Version
273
- version: 1.2.1
290
+ version: 3.5.0
274
291
  - !ruby/object:Gem::Dependency
275
292
  name: coveralls
276
293
  requirement: !ruby/object:Gem::Requirement
@@ -367,9 +384,9 @@ required_ruby_version: !ruby/object:Gem::Requirement
367
384
  version: '0'
368
385
  required_rubygems_version: !ruby/object:Gem::Requirement
369
386
  requirements:
370
- - - ">"
387
+ - - ">="
371
388
  - !ruby/object:Gem::Version
372
- version: 1.3.1
389
+ version: '0'
373
390
  requirements: []
374
391
  rubyforge_project:
375
392
  rubygems_version: 2.4.6