bio-gadget 0.2.1 → 0.2.2
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- data/lib/bio-gadget/demlt.rb +3 -3
- data/lib/bio-gadget/version.rb +1 -1
- metadata +2 -2
data/lib/bio-gadget/demlt.rb
CHANGED
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@@ -32,7 +32,7 @@ module Bio
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32
32
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ts = Array.new
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33
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qs = Array.new
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34
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(wells + ['other']).each { |well|
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35
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-
q = SizedQueue.new(
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35
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+
q = SizedQueue.new(1000)
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36
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t = Thread.new(well, q) do |well, q|
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tc = Thread.current
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tc[:file] = "#{options['output-dir']}/#{well}.fq.xz"
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@@ -52,7 +52,7 @@ module Bio
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ts.push(t)
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}
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55
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-
rq =
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55
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+
rq = SizedQueue.new(1000)
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Thread.new(rq) {
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Bio::Faster.new(:stdin).each_record(:quality => :raw) do |seqid, seq, qvs|
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rq.push([seqid, seq, qvs])
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@@ -65,7 +65,7 @@ module Bio
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if vals != ""
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seqs.push(vals)
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end
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68
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-
if vals == "" || seqs.size ==
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68
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+
if vals == "" || seqs.size == 10000 * Parallel.processor_count
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parallel_Levenshtein(seqs, bcs, ofs, bclen, qs)
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seqs = Array.new
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end
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data/lib/bio-gadget/version.rb
CHANGED
metadata
CHANGED
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@@ -1,7 +1,7 @@
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1
1
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--- !ruby/object:Gem::Specification
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2
2
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name: bio-gadget
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3
3
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version: !ruby/object:Gem::Version
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4
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-
version: 0.2.
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4
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+
version: 0.2.2
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5
5
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prerelease:
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6
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platform: ruby
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7
7
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authors:
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@@ -9,7 +9,7 @@ authors:
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autorequire:
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bindir: bin
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cert_chain: []
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12
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-
date: 2012-12-
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12
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+
date: 2012-12-13 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: gthor
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