finishm 0.0.4 → 0.0.5
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- checksums.yaml +4 -4
- data/VERSION +1 -1
- data/finishm.gemspec +3 -3
- data/lib/finishm/roundup.rb +1 -1
- metadata +2 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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1
1
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---
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2
2
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SHA1:
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3
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-
metadata.gz:
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4
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-
data.tar.gz:
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3
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+
metadata.gz: bce8ed121a1616212425ca92cee7529b7beba70b
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4
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+
data.tar.gz: cb79976079b563c129779f06d2b0bf94ebf2d093
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5
5
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SHA512:
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6
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-
metadata.gz:
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7
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-
data.tar.gz:
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6
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+
metadata.gz: 57b3a51e694974c24ff4f37005d8c111bfabd81421c16e35a0db57ccfc187e7752bd1214d457e356e88b98122e28b4f2f3cfc2c24ddf8253119b1d3e53f242d2
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7
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+
data.tar.gz: 508d9fb04d255a3d5fc597abdd8a86a42ca4b0298c16c8fcf5eaeaa8f5391c2210735bb7bd20e082ce1c08db73216fa52099983147bd06ee11c772de2bc8aed0
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data/VERSION
CHANGED
@@ -1 +1 @@
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1
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-
0.0.
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1
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+
0.0.5
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data/finishm.gemspec
CHANGED
@@ -2,17 +2,17 @@
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2
2
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# DO NOT EDIT THIS FILE DIRECTLY
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3
3
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# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
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4
4
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# -*- encoding: utf-8 -*-
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5
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-
# stub: finishm 0.0.
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5
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+
# stub: finishm 0.0.5 ruby lib
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6
6
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# stub: ext/mkrf_conf.rb
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7
7
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8
8
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Gem::Specification.new do |s|
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9
9
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s.name = "finishm"
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10
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-
s.version = "0.0.
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10
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+
s.version = "0.0.5"
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11
11
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12
12
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s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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13
13
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s.require_paths = ["lib"]
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14
14
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s.authors = ["Ben J. Woodcroft"]
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15
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-
s.date = "2015-08-
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15
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+
s.date = "2015-08-31"
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16
16
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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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17
17
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s.email = "donttrustben near gmail.com"
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18
18
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s.executables = ["finishm"]
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data/lib/finishm/roundup.rb
CHANGED
@@ -326,7 +326,7 @@ the finishm_roundup_results directory in FASTA format. The procedure is then rep
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|
326
326
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return gapfilled_sequence, num_gapfills, all_variants
|
327
327
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end
|
328
328
|
|
329
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-
def piece_together_gapfill(printer, master_graph, first_sequence, aconn, second_sequence, gap_length, max_gapfill_paths, options)
|
329
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+
def piece_together_gapfill(printer, master_graph, first_sequence, aconn, second_sequence, gap_length, max_gapfill_paths, options={})
|
330
330
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scaffold_sequence = nil
|
331
331
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gapfilled = -1
|
332
332
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if aconn.paths.length == 0 or aconn.paths.length > max_gapfill_paths
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metadata
CHANGED
@@ -1,14 +1,14 @@
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1
1
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--- !ruby/object:Gem::Specification
|
2
2
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name: finishm
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3
3
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version: !ruby/object:Gem::Version
|
4
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-
version: 0.0.
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4
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+
version: 0.0.5
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5
5
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platform: ruby
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6
6
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authors:
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7
7
|
- Ben J. Woodcroft
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8
8
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autorequire:
|
9
9
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bindir: bin
|
10
10
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cert_chain: []
|
11
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-
date: 2015-08-
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11
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+
date: 2015-08-31 00:00:00.000000000 Z
|
12
12
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dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
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name: bio-ipcress
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