finishm 0.0.4 → 0.0.5

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data/VERSION CHANGED
@@ -1 +1 @@
1
- 0.0.4
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+ 0.0.5
@@ -2,17 +2,17 @@
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  # DO NOT EDIT THIS FILE DIRECTLY
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  # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
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  # -*- encoding: utf-8 -*-
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- # stub: finishm 0.0.4 ruby lib
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+ # stub: finishm 0.0.5 ruby lib
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  # stub: ext/mkrf_conf.rb
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  Gem::Specification.new do |s|
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  s.name = "finishm"
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- s.version = "0.0.4"
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+ s.version = "0.0.5"
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  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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  s.require_paths = ["lib"]
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  s.authors = ["Ben J. Woodcroft"]
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- s.date = "2015-08-30"
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+ s.date = "2015-08-31"
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  s.description = "De-novo assemblies generally only provide draft genomes. FinishM is aimed at improving these draft assemblies."
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  s.email = "donttrustben near gmail.com"
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  s.executables = ["finishm"]
@@ -326,7 +326,7 @@ the finishm_roundup_results directory in FASTA format. The procedure is then rep
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  return gapfilled_sequence, num_gapfills, all_variants
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  end
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329
- def piece_together_gapfill(printer, master_graph, first_sequence, aconn, second_sequence, gap_length, max_gapfill_paths, options)
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+ def piece_together_gapfill(printer, master_graph, first_sequence, aconn, second_sequence, gap_length, max_gapfill_paths, options={})
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  scaffold_sequence = nil
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  gapfilled = -1
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  if aconn.paths.length == 0 or aconn.paths.length > max_gapfill_paths
metadata CHANGED
@@ -1,14 +1,14 @@
1
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  --- !ruby/object:Gem::Specification
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  name: finishm
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  version: !ruby/object:Gem::Version
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- version: 0.0.4
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+ version: 0.0.5
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  platform: ruby
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  authors:
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  - Ben J. Woodcroft
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  autorequire:
9
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  bindir: bin
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  cert_chain: []
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- date: 2015-08-30 00:00:00.000000000 Z
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+ date: 2015-08-31 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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14
  name: bio-ipcress