transrate 0.0.2 → 0.0.3

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@@ -2,15 +2,17 @@ module Transrate
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  class Transrater
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- def initialize path
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- @assembly = Assembly.new path
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+ def initialize assembly, reference, left, right, insertsize=nil, insertsd=nil
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+ @assembly = Assembly.new assembly
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+ @reference = Assembly.new reference
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  @read_metrics = ReadMetrics.new @assembly
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- @comparative_metrics = ComparativeMetrics.new @assembly
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+ @comparative_metrics = ComparativeMetrics.new(@assembly, @reference)
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+ self.run(left, right, insertsize, insertsd)
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  end
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- def run
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+ def run left, right, insertsize=nil, insertsd=nil
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  @assembly.run
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- @read_metrics.run
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+ @read_metrics.run(left, right)
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  @comparative_metrics.run
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  end
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@@ -4,7 +4,7 @@ module Transrate
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  module VERSION
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  MAJOR = 0
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  MINOR = 0
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- PATCH = 2
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+ PATCH = 3
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  BUILD = nil
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  STRING = [MAJOR, MINOR, PATCH, BUILD].compact.join('.')
metadata CHANGED
@@ -1,7 +1,7 @@
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  --- !ruby/object:Gem::Specification
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  name: transrate
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  version: !ruby/object:Gem::Version
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- version: 0.0.2
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+ version: 0.0.3
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  prerelease:
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  platform: ruby
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  authors: