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
@@ -32,7 +32,7 @@ module Bio
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|
32
32
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ts = Array.new
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33
33
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qs = Array.new
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34
34
|
(wells + ['other']).each { |well|
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35
|
-
q = SizedQueue.new(
|
35
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+
q = SizedQueue.new(1000)
|
36
36
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t = Thread.new(well, q) do |well, q|
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37
37
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tc = Thread.current
|
38
38
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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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52
52
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ts.push(t)
|
53
53
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}
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54
54
|
|
55
|
-
rq =
|
55
|
+
rq = SizedQueue.new(1000)
|
56
56
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Thread.new(rq) {
|
57
57
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Bio::Faster.new(:stdin).each_record(:quality => :raw) do |seqid, seq, qvs|
|
58
58
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rq.push([seqid, seq, qvs])
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@@ -65,7 +65,7 @@ module Bio
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|
65
65
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if vals != ""
|
66
66
|
seqs.push(vals)
|
67
67
|
end
|
68
|
-
if vals == "" || seqs.size ==
|
68
|
+
if vals == "" || seqs.size == 10000 * Parallel.processor_count
|
69
69
|
parallel_Levenshtein(seqs, bcs, ofs, bclen, qs)
|
70
70
|
seqs = Array.new
|
71
71
|
end
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data/lib/bio-gadget/version.rb
CHANGED
metadata
CHANGED
@@ -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
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 0.2.
|
4
|
+
version: 0.2.2
|
5
5
|
prerelease:
|
6
6
|
platform: ruby
|
7
7
|
authors:
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@@ -9,7 +9,7 @@ authors:
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|
9
9
|
autorequire:
|
10
10
|
bindir: bin
|
11
11
|
cert_chain: []
|
12
|
-
date: 2012-12-
|
12
|
+
date: 2012-12-13 00:00:00.000000000 Z
|
13
13
|
dependencies:
|
14
14
|
- !ruby/object:Gem::Dependency
|
15
15
|
name: gthor
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