finishm 0.0.1 → 0.0.2
Sign up to get free protection for your applications and to get access to all the features.
- checksums.yaml +4 -4
- data/Gemfile +19 -19
- data/VERSION +1 -1
- data/finishm.gemspec +631 -0
- data/lib/assembly/graph_generator.rb +0 -1
- data/lib/assembly/probed_graph.rb +0 -1
- metadata +99 -96
- data/bin/assembly_visualiser +0 -106
- data/bin/check_primer_combinations.rb +0 -73
- data/bin/contig_joiner.rb +0 -244
- data/bin/contigs_against_assembly.rb +0 -153
- data/bin/finishm_assembler +0 -55
- data/bin/finishm_gap_closer.rb +0 -241
- data/bin/kmer_abundance_file_tool.rb +0 -49
- data/bin/kmer_pattern_to_assembly.rb +0 -377
- data/bin/kmer_profile_finder.rb +0 -92
- data/bin/kmers_count_parse.d +0 -52
- data/bin/kmers_count_tabulate.d +0 -123
- data/bin/kmers_count_tabulate.rb +0 -84
- data/bin/pcr_result_parser.rb +0 -108
- data/bin/primer_finder.rb +0 -119
- data/bin/read_selection_by_kmer.d +0 -174
- data/bin/scaffold_by_pattern.rb +0 -119
- data/bin/scaffold_connection_possibilities_to_knowns.rb +0 -193
- data/bin/scaffold_end_coverages.rb +0 -69
- data/bin/trail_validator.rb +0 -84
checksums.yaml
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
---
|
|
2
2
|
SHA1:
|
|
3
|
-
metadata.gz:
|
|
4
|
-
data.tar.gz:
|
|
3
|
+
metadata.gz: d4185d82df8d5de264dee94a05867f051d0332b1
|
|
4
|
+
data.tar.gz: 313d7fd065da5b8fb74e3acd1ed0ed6a20f2b827
|
|
5
5
|
SHA512:
|
|
6
|
-
metadata.gz:
|
|
7
|
-
data.tar.gz:
|
|
6
|
+
metadata.gz: 0e74180aa4d37ee0307d86ab8352d63531612a76be161366d83e4dbc09a7bfc71d42f0152bafc3e503a5ae5bba6bd00040299d2d0a38717266c8a36a5f873a9c
|
|
7
|
+
data.tar.gz: 42237938390eb63124b5e9cc33fd01fc69d6ca354117c4745b13980d6f149fbeb0f9759eb36b91701d2f97bfb02a47a9e5cd800837e87d578eb712e06a889581
|
data/Gemfile
CHANGED
|
@@ -2,30 +2,30 @@ source "http://rubygems.org"
|
|
|
2
2
|
# Add dependencies required to use your gem here.
|
|
3
3
|
# Example:
|
|
4
4
|
# gem "activesupport", ">= 2.3.5"
|
|
5
|
-
gem 'bio-ipcress'
|
|
6
|
-
gem 'bio-logger'
|
|
7
|
-
gem 'bio'
|
|
8
|
-
gem 'progressbar'
|
|
9
|
-
gem 'bio-samtools'
|
|
10
|
-
gem 'ruby-graphviz'
|
|
11
|
-
gem 'ds'
|
|
12
|
-
gem 'hopcsv', '~> 0.4'
|
|
5
|
+
gem 'bio-ipcress', '~>0.0'
|
|
6
|
+
gem 'bio-logger', '~>1.0'
|
|
7
|
+
gem 'bio', '~>1.4', '>=1.4.3'
|
|
8
|
+
gem 'progressbar', '~>0.21'
|
|
9
|
+
gem 'bio-samtools', '~>0.6'
|
|
10
|
+
gem 'ruby-graphviz', '~>1.0', '>=1.0.9'
|
|
11
|
+
gem 'ds', '~>0.0', '>=0.0.4'
|
|
12
|
+
gem 'hopcsv', '~> 0.4', '>=0.4.3'
|
|
13
13
|
gem 'bio-velvet', '~>0.6'
|
|
14
14
|
gem 'bio-velvet_underground', '~>0.3'
|
|
15
|
-
gem 'ruby-progressbar'
|
|
16
|
-
gem 'yargraph', '~>0.0.4'
|
|
15
|
+
gem 'ruby-progressbar', '~>1.4', '>=1.4.2'
|
|
16
|
+
gem 'yargraph', '~>0.0', '>=0.0.4'
|
|
17
17
|
|
|
18
|
-
#only needed
|
|
19
|
-
|
|
18
|
+
# Really only needed for debug but there is the --debug modes in e.g. roundup
|
|
19
|
+
# so keeping it in here
|
|
20
|
+
gem 'pry', '~>0.10'
|
|
20
21
|
|
|
21
22
|
# Add dependencies to develop your gem here.
|
|
22
23
|
# Include everything needed to run rake, tests, features, etc.
|
|
23
24
|
group :development do
|
|
24
|
-
gem "rspec", ">= 2.8.0"
|
|
25
|
-
gem "yard", "
|
|
26
|
-
gem "rdoc", "
|
|
27
|
-
gem "bundler", ">=
|
|
28
|
-
gem 'jeweler'
|
|
29
|
-
gem 'bio-commandeer'
|
|
30
|
-
gem 'pry'
|
|
25
|
+
gem "rspec", '~>2.8', ">= 2.8.0"
|
|
26
|
+
gem "yard", "~>0.7"
|
|
27
|
+
gem "rdoc", "~>3.12"
|
|
28
|
+
gem "bundler", "~>1.6", '>=1.6.2'
|
|
29
|
+
gem 'jeweler', '~>2.0', '>=2.0.1'
|
|
30
|
+
gem 'bio-commandeer', '~>0.1'
|
|
31
31
|
end
|
data/VERSION
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
0.0.
|
|
1
|
+
0.0.2
|
data/finishm.gemspec
ADDED
|
@@ -0,0 +1,631 @@
|
|
|
1
|
+
# Generated by jeweler
|
|
2
|
+
# DO NOT EDIT THIS FILE DIRECTLY
|
|
3
|
+
# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
|
|
4
|
+
# -*- encoding: utf-8 -*-
|
|
5
|
+
# stub: finishm 0.0.2 ruby lib
|
|
6
|
+
# stub: ext/mkrf_conf.rb
|
|
7
|
+
|
|
8
|
+
Gem::Specification.new do |s|
|
|
9
|
+
s.name = "finishm"
|
|
10
|
+
s.version = "0.0.2"
|
|
11
|
+
|
|
12
|
+
s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
|
|
13
|
+
s.require_paths = ["lib"]
|
|
14
|
+
s.authors = ["Ben J. Woodcroft"]
|
|
15
|
+
s.date = "2015-07-30"
|
|
16
|
+
s.description = "De-novo assemblies generally only provide draft genomes. FinishM is aimed at improving these draft assemblies."
|
|
17
|
+
s.email = "donttrustben near gmail.com"
|
|
18
|
+
s.executables = ["finishm"]
|
|
19
|
+
s.extensions = ["ext/mkrf_conf.rb"]
|
|
20
|
+
s.extra_rdoc_files = [
|
|
21
|
+
"LICENSE.txt",
|
|
22
|
+
"README.md"
|
|
23
|
+
]
|
|
24
|
+
s.files = [
|
|
25
|
+
".document",
|
|
26
|
+
".gitmodules",
|
|
27
|
+
".rspec",
|
|
28
|
+
"Gemfile",
|
|
29
|
+
"LICENSE.txt",
|
|
30
|
+
"README.md",
|
|
31
|
+
"Rakefile",
|
|
32
|
+
"VERSION",
|
|
33
|
+
"bin/finishm",
|
|
34
|
+
"ext/mkrf_conf.rb",
|
|
35
|
+
"ext/src/Makefile",
|
|
36
|
+
"ext/src/src/allocArray.c",
|
|
37
|
+
"ext/src/src/allocArray.h",
|
|
38
|
+
"ext/src/src/autoOpen.c",
|
|
39
|
+
"ext/src/src/autoOpen.h",
|
|
40
|
+
"ext/src/src/binarySequences.c",
|
|
41
|
+
"ext/src/src/binarySequences.h",
|
|
42
|
+
"ext/src/src/concatenatedGraph.c",
|
|
43
|
+
"ext/src/src/concatenatedGraph.h",
|
|
44
|
+
"ext/src/src/concatenatedPreGraph.c",
|
|
45
|
+
"ext/src/src/concatenatedPreGraph.h",
|
|
46
|
+
"ext/src/src/correctedGraph.c",
|
|
47
|
+
"ext/src/src/correctedGraph.h",
|
|
48
|
+
"ext/src/src/dfib.c",
|
|
49
|
+
"ext/src/src/dfib.h",
|
|
50
|
+
"ext/src/src/dfibHeap.c",
|
|
51
|
+
"ext/src/src/dfibHeap.h",
|
|
52
|
+
"ext/src/src/dfibpriv.h",
|
|
53
|
+
"ext/src/src/fib.c",
|
|
54
|
+
"ext/src/src/fib.h",
|
|
55
|
+
"ext/src/src/fibHeap.c",
|
|
56
|
+
"ext/src/src/fibHeap.h",
|
|
57
|
+
"ext/src/src/fibpriv.h",
|
|
58
|
+
"ext/src/src/globals.h",
|
|
59
|
+
"ext/src/src/graph.c",
|
|
60
|
+
"ext/src/src/graph.h",
|
|
61
|
+
"ext/src/src/graphReConstruction.c",
|
|
62
|
+
"ext/src/src/graphReConstruction.h",
|
|
63
|
+
"ext/src/src/graphStats.c",
|
|
64
|
+
"ext/src/src/graphStats.h",
|
|
65
|
+
"ext/src/src/graphStructures.h",
|
|
66
|
+
"ext/src/src/kmer.c",
|
|
67
|
+
"ext/src/src/kmer.h",
|
|
68
|
+
"ext/src/src/kmerOccurenceTable.c",
|
|
69
|
+
"ext/src/src/kmerOccurenceTable.h",
|
|
70
|
+
"ext/src/src/kseq.h",
|
|
71
|
+
"ext/src/src/locallyCorrectedGraph.c",
|
|
72
|
+
"ext/src/src/locallyCorrectedGraph.h",
|
|
73
|
+
"ext/src/src/passageMarker.c",
|
|
74
|
+
"ext/src/src/passageMarker.h",
|
|
75
|
+
"ext/src/src/preGraph.c",
|
|
76
|
+
"ext/src/src/preGraph.h",
|
|
77
|
+
"ext/src/src/preGraphConstruction.c",
|
|
78
|
+
"ext/src/src/preGraphConstruction.h",
|
|
79
|
+
"ext/src/src/probe_node_finder.c",
|
|
80
|
+
"ext/src/src/probe_node_finder.h",
|
|
81
|
+
"ext/src/src/readCoherentGraph.c",
|
|
82
|
+
"ext/src/src/readCoherentGraph.h",
|
|
83
|
+
"ext/src/src/readSet.c",
|
|
84
|
+
"ext/src/src/readSet.h",
|
|
85
|
+
"ext/src/src/readToNode.c",
|
|
86
|
+
"ext/src/src/readToNode.h",
|
|
87
|
+
"ext/src/src/recycleBin.c",
|
|
88
|
+
"ext/src/src/recycleBin.h",
|
|
89
|
+
"ext/src/src/roadMap.c",
|
|
90
|
+
"ext/src/src/roadMap.h",
|
|
91
|
+
"ext/src/src/run.c",
|
|
92
|
+
"ext/src/src/run.h",
|
|
93
|
+
"ext/src/src/run2.c",
|
|
94
|
+
"ext/src/src/runReadToNode.c",
|
|
95
|
+
"ext/src/src/scaffold.c",
|
|
96
|
+
"ext/src/src/scaffold.h",
|
|
97
|
+
"ext/src/src/shortReadPairs.c",
|
|
98
|
+
"ext/src/src/shortReadPairs.h",
|
|
99
|
+
"ext/src/src/splay.c",
|
|
100
|
+
"ext/src/src/splay.h",
|
|
101
|
+
"ext/src/src/splayTable.c",
|
|
102
|
+
"ext/src/src/splayTable.h",
|
|
103
|
+
"ext/src/src/tightString.c",
|
|
104
|
+
"ext/src/src/tightString.h",
|
|
105
|
+
"ext/src/src/utility.c",
|
|
106
|
+
"ext/src/src/utility.h",
|
|
107
|
+
"ext/src/third-party/zlib-1.2.3/ChangeLog",
|
|
108
|
+
"ext/src/third-party/zlib-1.2.3/FAQ",
|
|
109
|
+
"ext/src/third-party/zlib-1.2.3/INDEX",
|
|
110
|
+
"ext/src/third-party/zlib-1.2.3/Makefile",
|
|
111
|
+
"ext/src/third-party/zlib-1.2.3/Makefile.in",
|
|
112
|
+
"ext/src/third-party/zlib-1.2.3/README",
|
|
113
|
+
"ext/src/third-party/zlib-1.2.3/adler32.c",
|
|
114
|
+
"ext/src/third-party/zlib-1.2.3/adler32.o",
|
|
115
|
+
"ext/src/third-party/zlib-1.2.3/algorithm.txt",
|
|
116
|
+
"ext/src/third-party/zlib-1.2.3/amiga/Makefile.pup",
|
|
117
|
+
"ext/src/third-party/zlib-1.2.3/amiga/Makefile.sas",
|
|
118
|
+
"ext/src/third-party/zlib-1.2.3/as400/bndsrc",
|
|
119
|
+
"ext/src/third-party/zlib-1.2.3/as400/compile.clp",
|
|
120
|
+
"ext/src/third-party/zlib-1.2.3/as400/readme.txt",
|
|
121
|
+
"ext/src/third-party/zlib-1.2.3/as400/zlib.inc",
|
|
122
|
+
"ext/src/third-party/zlib-1.2.3/compress.c",
|
|
123
|
+
"ext/src/third-party/zlib-1.2.3/compress.o",
|
|
124
|
+
"ext/src/third-party/zlib-1.2.3/configure",
|
|
125
|
+
"ext/src/third-party/zlib-1.2.3/contrib/README.contrib",
|
|
126
|
+
"ext/src/third-party/zlib-1.2.3/contrib/ada/buffer_demo.adb",
|
|
127
|
+
"ext/src/third-party/zlib-1.2.3/contrib/ada/mtest.adb",
|
|
128
|
+
"ext/src/third-party/zlib-1.2.3/contrib/ada/read.adb",
|
|
129
|
+
"ext/src/third-party/zlib-1.2.3/contrib/ada/readme.txt",
|
|
130
|
+
"ext/src/third-party/zlib-1.2.3/contrib/ada/test.adb",
|
|
131
|
+
"ext/src/third-party/zlib-1.2.3/contrib/ada/zlib-streams.adb",
|
|
132
|
+
"ext/src/third-party/zlib-1.2.3/contrib/ada/zlib-streams.ads",
|
|
133
|
+
"ext/src/third-party/zlib-1.2.3/contrib/ada/zlib-thin.adb",
|
|
134
|
+
"ext/src/third-party/zlib-1.2.3/contrib/ada/zlib-thin.ads",
|
|
135
|
+
"ext/src/third-party/zlib-1.2.3/contrib/ada/zlib.adb",
|
|
136
|
+
"ext/src/third-party/zlib-1.2.3/contrib/ada/zlib.ads",
|
|
137
|
+
"ext/src/third-party/zlib-1.2.3/contrib/ada/zlib.gpr",
|
|
138
|
+
"ext/src/third-party/zlib-1.2.3/contrib/asm586/README.586",
|
|
139
|
+
"ext/src/third-party/zlib-1.2.3/contrib/asm586/match.S",
|
|
140
|
+
"ext/src/third-party/zlib-1.2.3/contrib/asm686/README.686",
|
|
141
|
+
"ext/src/third-party/zlib-1.2.3/contrib/asm686/match.S",
|
|
142
|
+
"ext/src/third-party/zlib-1.2.3/contrib/blast/Makefile",
|
|
143
|
+
"ext/src/third-party/zlib-1.2.3/contrib/blast/README",
|
|
144
|
+
"ext/src/third-party/zlib-1.2.3/contrib/blast/blast.c",
|
|
145
|
+
"ext/src/third-party/zlib-1.2.3/contrib/blast/blast.h",
|
|
146
|
+
"ext/src/third-party/zlib-1.2.3/contrib/blast/test.pk",
|
|
147
|
+
"ext/src/third-party/zlib-1.2.3/contrib/blast/test.txt",
|
|
148
|
+
"ext/src/third-party/zlib-1.2.3/contrib/delphi/ZLib.pas",
|
|
149
|
+
"ext/src/third-party/zlib-1.2.3/contrib/delphi/ZLibConst.pas",
|
|
150
|
+
"ext/src/third-party/zlib-1.2.3/contrib/delphi/readme.txt",
|
|
151
|
+
"ext/src/third-party/zlib-1.2.3/contrib/delphi/zlibd32.mak",
|
|
152
|
+
"ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib.build",
|
|
153
|
+
"ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib.chm",
|
|
154
|
+
"ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib.sln",
|
|
155
|
+
"ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/AssemblyInfo.cs",
|
|
156
|
+
"ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/ChecksumImpl.cs",
|
|
157
|
+
"ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/CircularBuffer.cs",
|
|
158
|
+
"ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/CodecBase.cs",
|
|
159
|
+
"ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/Deflater.cs",
|
|
160
|
+
"ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/DotZLib.cs",
|
|
161
|
+
"ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/DotZLib.csproj",
|
|
162
|
+
"ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/GZipStream.cs",
|
|
163
|
+
"ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/Inflater.cs",
|
|
164
|
+
"ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/UnitTests.cs",
|
|
165
|
+
"ext/src/third-party/zlib-1.2.3/contrib/dotzlib/LICENSE_1_0.txt",
|
|
166
|
+
"ext/src/third-party/zlib-1.2.3/contrib/dotzlib/readme.txt",
|
|
167
|
+
"ext/src/third-party/zlib-1.2.3/contrib/infback9/README",
|
|
168
|
+
"ext/src/third-party/zlib-1.2.3/contrib/infback9/infback9.c",
|
|
169
|
+
"ext/src/third-party/zlib-1.2.3/contrib/infback9/infback9.h",
|
|
170
|
+
"ext/src/third-party/zlib-1.2.3/contrib/infback9/inffix9.h",
|
|
171
|
+
"ext/src/third-party/zlib-1.2.3/contrib/infback9/inflate9.h",
|
|
172
|
+
"ext/src/third-party/zlib-1.2.3/contrib/infback9/inftree9.c",
|
|
173
|
+
"ext/src/third-party/zlib-1.2.3/contrib/infback9/inftree9.h",
|
|
174
|
+
"ext/src/third-party/zlib-1.2.3/contrib/inflate86/inffas86.c",
|
|
175
|
+
"ext/src/third-party/zlib-1.2.3/contrib/inflate86/inffast.S",
|
|
176
|
+
"ext/src/third-party/zlib-1.2.3/contrib/iostream/test.cpp",
|
|
177
|
+
"ext/src/third-party/zlib-1.2.3/contrib/iostream/zfstream.cpp",
|
|
178
|
+
"ext/src/third-party/zlib-1.2.3/contrib/iostream/zfstream.h",
|
|
179
|
+
"ext/src/third-party/zlib-1.2.3/contrib/iostream2/zstream.h",
|
|
180
|
+
"ext/src/third-party/zlib-1.2.3/contrib/iostream2/zstream_test.cpp",
|
|
181
|
+
"ext/src/third-party/zlib-1.2.3/contrib/iostream3/README",
|
|
182
|
+
"ext/src/third-party/zlib-1.2.3/contrib/iostream3/TODO",
|
|
183
|
+
"ext/src/third-party/zlib-1.2.3/contrib/iostream3/test.cc",
|
|
184
|
+
"ext/src/third-party/zlib-1.2.3/contrib/iostream3/zfstream.cc",
|
|
185
|
+
"ext/src/third-party/zlib-1.2.3/contrib/iostream3/zfstream.h",
|
|
186
|
+
"ext/src/third-party/zlib-1.2.3/contrib/masm686/match.asm",
|
|
187
|
+
"ext/src/third-party/zlib-1.2.3/contrib/masmx64/bld_ml64.bat",
|
|
188
|
+
"ext/src/third-party/zlib-1.2.3/contrib/masmx64/gvmat64.asm",
|
|
189
|
+
"ext/src/third-party/zlib-1.2.3/contrib/masmx64/gvmat64.obj",
|
|
190
|
+
"ext/src/third-party/zlib-1.2.3/contrib/masmx64/inffas8664.c",
|
|
191
|
+
"ext/src/third-party/zlib-1.2.3/contrib/masmx64/inffasx64.asm",
|
|
192
|
+
"ext/src/third-party/zlib-1.2.3/contrib/masmx64/inffasx64.obj",
|
|
193
|
+
"ext/src/third-party/zlib-1.2.3/contrib/masmx64/readme.txt",
|
|
194
|
+
"ext/src/third-party/zlib-1.2.3/contrib/masmx86/bld_ml32.bat",
|
|
195
|
+
"ext/src/third-party/zlib-1.2.3/contrib/masmx86/gvmat32.asm",
|
|
196
|
+
"ext/src/third-party/zlib-1.2.3/contrib/masmx86/gvmat32.obj",
|
|
197
|
+
"ext/src/third-party/zlib-1.2.3/contrib/masmx86/gvmat32c.c",
|
|
198
|
+
"ext/src/third-party/zlib-1.2.3/contrib/masmx86/inffas32.asm",
|
|
199
|
+
"ext/src/third-party/zlib-1.2.3/contrib/masmx86/inffas32.obj",
|
|
200
|
+
"ext/src/third-party/zlib-1.2.3/contrib/masmx86/mkasm.bat",
|
|
201
|
+
"ext/src/third-party/zlib-1.2.3/contrib/masmx86/readme.txt",
|
|
202
|
+
"ext/src/third-party/zlib-1.2.3/contrib/minizip/ChangeLogUnzip",
|
|
203
|
+
"ext/src/third-party/zlib-1.2.3/contrib/minizip/Makefile",
|
|
204
|
+
"ext/src/third-party/zlib-1.2.3/contrib/minizip/crypt.h",
|
|
205
|
+
"ext/src/third-party/zlib-1.2.3/contrib/minizip/ioapi.c",
|
|
206
|
+
"ext/src/third-party/zlib-1.2.3/contrib/minizip/ioapi.h",
|
|
207
|
+
"ext/src/third-party/zlib-1.2.3/contrib/minizip/iowin32.c",
|
|
208
|
+
"ext/src/third-party/zlib-1.2.3/contrib/minizip/iowin32.h",
|
|
209
|
+
"ext/src/third-party/zlib-1.2.3/contrib/minizip/miniunz.c",
|
|
210
|
+
"ext/src/third-party/zlib-1.2.3/contrib/minizip/minizip.c",
|
|
211
|
+
"ext/src/third-party/zlib-1.2.3/contrib/minizip/mztools.c",
|
|
212
|
+
"ext/src/third-party/zlib-1.2.3/contrib/minizip/mztools.h",
|
|
213
|
+
"ext/src/third-party/zlib-1.2.3/contrib/minizip/unzip.c",
|
|
214
|
+
"ext/src/third-party/zlib-1.2.3/contrib/minizip/unzip.h",
|
|
215
|
+
"ext/src/third-party/zlib-1.2.3/contrib/minizip/zip.c",
|
|
216
|
+
"ext/src/third-party/zlib-1.2.3/contrib/minizip/zip.h",
|
|
217
|
+
"ext/src/third-party/zlib-1.2.3/contrib/pascal/example.pas",
|
|
218
|
+
"ext/src/third-party/zlib-1.2.3/contrib/pascal/readme.txt",
|
|
219
|
+
"ext/src/third-party/zlib-1.2.3/contrib/pascal/zlibd32.mak",
|
|
220
|
+
"ext/src/third-party/zlib-1.2.3/contrib/pascal/zlibpas.pas",
|
|
221
|
+
"ext/src/third-party/zlib-1.2.3/contrib/puff/Makefile",
|
|
222
|
+
"ext/src/third-party/zlib-1.2.3/contrib/puff/README",
|
|
223
|
+
"ext/src/third-party/zlib-1.2.3/contrib/puff/puff.c",
|
|
224
|
+
"ext/src/third-party/zlib-1.2.3/contrib/puff/puff.h",
|
|
225
|
+
"ext/src/third-party/zlib-1.2.3/contrib/puff/zeros.raw",
|
|
226
|
+
"ext/src/third-party/zlib-1.2.3/contrib/testzlib/testzlib.c",
|
|
227
|
+
"ext/src/third-party/zlib-1.2.3/contrib/testzlib/testzlib.txt",
|
|
228
|
+
"ext/src/third-party/zlib-1.2.3/contrib/untgz/Makefile",
|
|
229
|
+
"ext/src/third-party/zlib-1.2.3/contrib/untgz/Makefile.msc",
|
|
230
|
+
"ext/src/third-party/zlib-1.2.3/contrib/untgz/untgz.c",
|
|
231
|
+
"ext/src/third-party/zlib-1.2.3/contrib/vstudio/readme.txt",
|
|
232
|
+
"ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/miniunz.vcproj",
|
|
233
|
+
"ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/minizip.vcproj",
|
|
234
|
+
"ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/testzlib.vcproj",
|
|
235
|
+
"ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/zlib.rc",
|
|
236
|
+
"ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/zlibstat.vcproj",
|
|
237
|
+
"ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/zlibvc.def",
|
|
238
|
+
"ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/zlibvc.sln",
|
|
239
|
+
"ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/zlibvc.vcproj",
|
|
240
|
+
"ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/miniunz.vcproj",
|
|
241
|
+
"ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/minizip.vcproj",
|
|
242
|
+
"ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/testzlib.vcproj",
|
|
243
|
+
"ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/testzlibdll.vcproj",
|
|
244
|
+
"ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/zlib.rc",
|
|
245
|
+
"ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/zlibstat.vcproj",
|
|
246
|
+
"ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/zlibvc.def",
|
|
247
|
+
"ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/zlibvc.sln",
|
|
248
|
+
"ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/zlibvc.vcproj",
|
|
249
|
+
"ext/src/third-party/zlib-1.2.3/crc32.c",
|
|
250
|
+
"ext/src/third-party/zlib-1.2.3/crc32.h",
|
|
251
|
+
"ext/src/third-party/zlib-1.2.3/crc32.o",
|
|
252
|
+
"ext/src/third-party/zlib-1.2.3/deflate.c",
|
|
253
|
+
"ext/src/third-party/zlib-1.2.3/deflate.h",
|
|
254
|
+
"ext/src/third-party/zlib-1.2.3/deflate.o",
|
|
255
|
+
"ext/src/third-party/zlib-1.2.3/example",
|
|
256
|
+
"ext/src/third-party/zlib-1.2.3/example.c",
|
|
257
|
+
"ext/src/third-party/zlib-1.2.3/examples/README.examples",
|
|
258
|
+
"ext/src/third-party/zlib-1.2.3/examples/fitblk.c",
|
|
259
|
+
"ext/src/third-party/zlib-1.2.3/examples/gun.c",
|
|
260
|
+
"ext/src/third-party/zlib-1.2.3/examples/gzappend.c",
|
|
261
|
+
"ext/src/third-party/zlib-1.2.3/examples/gzjoin.c",
|
|
262
|
+
"ext/src/third-party/zlib-1.2.3/examples/gzlog.c",
|
|
263
|
+
"ext/src/third-party/zlib-1.2.3/examples/gzlog.h",
|
|
264
|
+
"ext/src/third-party/zlib-1.2.3/examples/zlib_how.html",
|
|
265
|
+
"ext/src/third-party/zlib-1.2.3/examples/zpipe.c",
|
|
266
|
+
"ext/src/third-party/zlib-1.2.3/examples/zran.c",
|
|
267
|
+
"ext/src/third-party/zlib-1.2.3/gzio.c",
|
|
268
|
+
"ext/src/third-party/zlib-1.2.3/gzio.o",
|
|
269
|
+
"ext/src/third-party/zlib-1.2.3/infback.c",
|
|
270
|
+
"ext/src/third-party/zlib-1.2.3/infback.o",
|
|
271
|
+
"ext/src/third-party/zlib-1.2.3/inffast.c",
|
|
272
|
+
"ext/src/third-party/zlib-1.2.3/inffast.h",
|
|
273
|
+
"ext/src/third-party/zlib-1.2.3/inffast.o",
|
|
274
|
+
"ext/src/third-party/zlib-1.2.3/inffixed.h",
|
|
275
|
+
"ext/src/third-party/zlib-1.2.3/inflate.c",
|
|
276
|
+
"ext/src/third-party/zlib-1.2.3/inflate.h",
|
|
277
|
+
"ext/src/third-party/zlib-1.2.3/inflate.o",
|
|
278
|
+
"ext/src/third-party/zlib-1.2.3/inftrees.c",
|
|
279
|
+
"ext/src/third-party/zlib-1.2.3/inftrees.h",
|
|
280
|
+
"ext/src/third-party/zlib-1.2.3/inftrees.o",
|
|
281
|
+
"ext/src/third-party/zlib-1.2.3/libz.a",
|
|
282
|
+
"ext/src/third-party/zlib-1.2.3/make_vms.com",
|
|
283
|
+
"ext/src/third-party/zlib-1.2.3/minigzip",
|
|
284
|
+
"ext/src/third-party/zlib-1.2.3/minigzip.c",
|
|
285
|
+
"ext/src/third-party/zlib-1.2.3/msdos/Makefile.bor",
|
|
286
|
+
"ext/src/third-party/zlib-1.2.3/msdos/Makefile.dj2",
|
|
287
|
+
"ext/src/third-party/zlib-1.2.3/msdos/Makefile.emx",
|
|
288
|
+
"ext/src/third-party/zlib-1.2.3/msdos/Makefile.msc",
|
|
289
|
+
"ext/src/third-party/zlib-1.2.3/msdos/Makefile.tc",
|
|
290
|
+
"ext/src/third-party/zlib-1.2.3/old/Makefile.riscos",
|
|
291
|
+
"ext/src/third-party/zlib-1.2.3/old/README",
|
|
292
|
+
"ext/src/third-party/zlib-1.2.3/old/descrip.mms",
|
|
293
|
+
"ext/src/third-party/zlib-1.2.3/old/os2/Makefile.os2",
|
|
294
|
+
"ext/src/third-party/zlib-1.2.3/old/os2/zlib.def",
|
|
295
|
+
"ext/src/third-party/zlib-1.2.3/old/visual-basic.txt",
|
|
296
|
+
"ext/src/third-party/zlib-1.2.3/old/zlib.html",
|
|
297
|
+
"ext/src/third-party/zlib-1.2.3/projects/README.projects",
|
|
298
|
+
"ext/src/third-party/zlib-1.2.3/projects/visualc6/README.txt",
|
|
299
|
+
"ext/src/third-party/zlib-1.2.3/projects/visualc6/example.dsp",
|
|
300
|
+
"ext/src/third-party/zlib-1.2.3/projects/visualc6/minigzip.dsp",
|
|
301
|
+
"ext/src/third-party/zlib-1.2.3/projects/visualc6/zlib.dsp",
|
|
302
|
+
"ext/src/third-party/zlib-1.2.3/projects/visualc6/zlib.dsw",
|
|
303
|
+
"ext/src/third-party/zlib-1.2.3/qnx/package.qpg",
|
|
304
|
+
"ext/src/third-party/zlib-1.2.3/trees.c",
|
|
305
|
+
"ext/src/third-party/zlib-1.2.3/trees.h",
|
|
306
|
+
"ext/src/third-party/zlib-1.2.3/trees.o",
|
|
307
|
+
"ext/src/third-party/zlib-1.2.3/uncompr.c",
|
|
308
|
+
"ext/src/third-party/zlib-1.2.3/uncompr.o",
|
|
309
|
+
"ext/src/third-party/zlib-1.2.3/win32/DLL_FAQ.txt",
|
|
310
|
+
"ext/src/third-party/zlib-1.2.3/win32/Makefile.bor",
|
|
311
|
+
"ext/src/third-party/zlib-1.2.3/win32/Makefile.emx",
|
|
312
|
+
"ext/src/third-party/zlib-1.2.3/win32/Makefile.gcc",
|
|
313
|
+
"ext/src/third-party/zlib-1.2.3/win32/Makefile.msc",
|
|
314
|
+
"ext/src/third-party/zlib-1.2.3/win32/VisualC.txt",
|
|
315
|
+
"ext/src/third-party/zlib-1.2.3/win32/zlib.def",
|
|
316
|
+
"ext/src/third-party/zlib-1.2.3/win32/zlib1.rc",
|
|
317
|
+
"ext/src/third-party/zlib-1.2.3/zconf.h",
|
|
318
|
+
"ext/src/third-party/zlib-1.2.3/zconf.in.h",
|
|
319
|
+
"ext/src/third-party/zlib-1.2.3/zlib.3",
|
|
320
|
+
"ext/src/third-party/zlib-1.2.3/zlib.h",
|
|
321
|
+
"ext/src/third-party/zlib-1.2.3/zutil.c",
|
|
322
|
+
"ext/src/third-party/zlib-1.2.3/zutil.h",
|
|
323
|
+
"ext/src/third-party/zlib-1.2.3/zutil.o",
|
|
324
|
+
"finishm.gemspec",
|
|
325
|
+
"lib/assembly/a_b_visualiser.rb",
|
|
326
|
+
"lib/assembly/acyclic_connection_finder.rb",
|
|
327
|
+
"lib/assembly/all_orfs.rb",
|
|
328
|
+
"lib/assembly/bad_format_writer.rb",
|
|
329
|
+
"lib/assembly/bam_probe_read_selector.rb",
|
|
330
|
+
"lib/assembly/bubbly_assembler.rb",
|
|
331
|
+
"lib/assembly/c_probe_node_finder.rb",
|
|
332
|
+
"lib/assembly/connection_interpreter.rb",
|
|
333
|
+
"lib/assembly/contig_printer.rb",
|
|
334
|
+
"lib/assembly/coverage_based_graph_filter.rb",
|
|
335
|
+
"lib/assembly/depth_first_search.rb",
|
|
336
|
+
"lib/assembly/dijkstra.rb",
|
|
337
|
+
"lib/assembly/fluffer.rb",
|
|
338
|
+
"lib/assembly/graph_explorer.rb",
|
|
339
|
+
"lib/assembly/graph_generator.rb",
|
|
340
|
+
"lib/assembly/height_finder.rb",
|
|
341
|
+
"lib/assembly/hybrid_velvet_graph.rb",
|
|
342
|
+
"lib/assembly/input_genome.rb",
|
|
343
|
+
"lib/assembly/kmer_coverage_based_path_filter.rb",
|
|
344
|
+
"lib/assembly/node_finder.rb",
|
|
345
|
+
"lib/assembly/oriented_node_trail.rb",
|
|
346
|
+
"lib/assembly/paired_end_assembler.rb",
|
|
347
|
+
"lib/assembly/paired_end_neighbour_finder.rb",
|
|
348
|
+
"lib/assembly/probed_graph.rb",
|
|
349
|
+
"lib/assembly/read_input.rb",
|
|
350
|
+
"lib/assembly/read_to_node.rb",
|
|
351
|
+
"lib/assembly/scaffold_breaker.rb",
|
|
352
|
+
"lib/assembly/sequence_hasher.rb",
|
|
353
|
+
"lib/assembly/single_coherent_paths_between_nodes.rb",
|
|
354
|
+
"lib/assembly/single_coherent_wanderer.rb",
|
|
355
|
+
"lib/assembly/single_ended_assembler.rb",
|
|
356
|
+
"lib/assembly/velvet_c_binding.rb",
|
|
357
|
+
"lib/assembly/velvet_graph_sequence_extractor.rb",
|
|
358
|
+
"lib/external/VERSION",
|
|
359
|
+
"lib/finishm/assemble.rb",
|
|
360
|
+
"lib/finishm/explore.rb",
|
|
361
|
+
"lib/finishm/finisher.rb",
|
|
362
|
+
"lib/finishm/fluff.rb",
|
|
363
|
+
"lib/finishm/gapfiller.rb",
|
|
364
|
+
"lib/finishm/orfs_finder.rb",
|
|
365
|
+
"lib/finishm/path_counter.rb",
|
|
366
|
+
"lib/finishm/primers.rb",
|
|
367
|
+
"lib/finishm/primers_check.rb",
|
|
368
|
+
"lib/finishm/roundup.rb",
|
|
369
|
+
"lib/finishm/sequence.rb",
|
|
370
|
+
"lib/finishm/visualise.rb",
|
|
371
|
+
"lib/finishm/wander.rb",
|
|
372
|
+
"lib/kmer_abundance_pattern.rb",
|
|
373
|
+
"lib/kmer_multi_abundance_file.rb",
|
|
374
|
+
"lib/oligo_designer.rb",
|
|
375
|
+
"lib/priner.rb",
|
|
376
|
+
"spec/acyclic_connection_finder_spec.rb",
|
|
377
|
+
"spec/all_orfs_spec.rb",
|
|
378
|
+
"spec/assemble_spec.rb",
|
|
379
|
+
"spec/bubbly_assembler_spec.rb",
|
|
380
|
+
"spec/c_node_finder_spec.rb",
|
|
381
|
+
"spec/connection_interpreter_spec.rb",
|
|
382
|
+
"spec/contig_printer_spec.rb",
|
|
383
|
+
"spec/coverage_based_graph_filter_spec.rb",
|
|
384
|
+
"spec/data/6_3e4e5e6e.1vANME.bam",
|
|
385
|
+
"spec/data/6_3e4e5e6e.1vANME.bam.bai",
|
|
386
|
+
"spec/data/acyclic_connection_finder/1/probes.fa",
|
|
387
|
+
"spec/data/acyclic_connection_finder/1/random1.fa",
|
|
388
|
+
"spec/data/acyclic_connection_finder/1/random1.sammy.fa.gz",
|
|
389
|
+
"spec/data/acyclic_connection_finder/1/random2.fa",
|
|
390
|
+
"spec/data/acyclic_connection_finder/1/random2.sammy.fa.gz",
|
|
391
|
+
"spec/data/assembly/1_simple_bubble_uneven_coverage/random3000.fa",
|
|
392
|
+
"spec/data/assembly/1_simple_bubble_uneven_coverage/random3000.slightly_changed.fa",
|
|
393
|
+
"spec/data/assembly/1_simple_bubble_uneven_coverage/reads_combined.fa.gz",
|
|
394
|
+
"spec/data/assembly_visualiser/Contig_6_1_to_250.fa.kmers31",
|
|
395
|
+
"spec/data/assembly_visualiser/Contig_7_1_to_250.fa.kmers31",
|
|
396
|
+
"spec/data/assembly_visualiser/Graph",
|
|
397
|
+
"spec/data/assembly_visualiser/start_kmers1",
|
|
398
|
+
"spec/data/bands.csv",
|
|
399
|
+
"spec/data/c_probe_node_finder/1/CnyUnifiedSeq",
|
|
400
|
+
"spec/data/c_probe_node_finder/1/CnyUnifiedSeq.names",
|
|
401
|
+
"spec/data/c_probe_node_finder/1/Graph2",
|
|
402
|
+
"spec/data/c_probe_node_finder/1/LastGraph",
|
|
403
|
+
"spec/data/c_probe_node_finder/1/Log",
|
|
404
|
+
"spec/data/c_probe_node_finder/1/PreGraph",
|
|
405
|
+
"spec/data/c_probe_node_finder/1/Roadmaps",
|
|
406
|
+
"spec/data/c_probe_node_finder/1/contigs.fa",
|
|
407
|
+
"spec/data/c_probe_node_finder/1/stats.txt",
|
|
408
|
+
"spec/data/contig_printer/1/HOWTO_RECREATE",
|
|
409
|
+
"spec/data/contig_printer/1/contigs.fa",
|
|
410
|
+
"spec/data/contig_printer/1/seq.fa",
|
|
411
|
+
"spec/data/contig_printer/1/seq.fa.svg",
|
|
412
|
+
"spec/data/contig_printer/1/seq.fa.velvet/Graph2",
|
|
413
|
+
"spec/data/contig_printer/1/seq.fa.velvet/LastGraph",
|
|
414
|
+
"spec/data/contig_printer/1/seq.fa.velvet/Log",
|
|
415
|
+
"spec/data/contig_printer/1/seq.fa.velvet/PreGraph",
|
|
416
|
+
"spec/data/contig_printer/1/seq.fa.velvet/Roadmaps",
|
|
417
|
+
"spec/data/contig_printer/1/seq.fa.velvet/Sequences",
|
|
418
|
+
"spec/data/contig_printer/1/seq.fa.velvet/contigs.fa",
|
|
419
|
+
"spec/data/contig_printer/1/seq.fa.velvet/stats.txt",
|
|
420
|
+
"spec/data/contig_printer/1/seq.faVseq2_1to550.fa.bam",
|
|
421
|
+
"spec/data/contig_printer/1/seq.faVseq2_1to550.fa.bam.bai",
|
|
422
|
+
"spec/data/contig_printer/1/seq.node12.fa",
|
|
423
|
+
"spec/data/contig_printer/1/seq1_1to550.fa",
|
|
424
|
+
"spec/data/contig_printer/1/seq2_1to550.fa",
|
|
425
|
+
"spec/data/contig_printer/1/seq2_1to550.fa.fai",
|
|
426
|
+
"spec/data/explore/1/2seqs.sammy.fa",
|
|
427
|
+
"spec/data/explore/1/HOWTO_RECREATE.txt",
|
|
428
|
+
"spec/data/explore/1/a.fa",
|
|
429
|
+
"spec/data/explore/1/seq1_and_a.fa",
|
|
430
|
+
"spec/data/explore/1/seq2.fa",
|
|
431
|
+
"spec/data/fluff/1/2seqs.sammy.fa",
|
|
432
|
+
"spec/data/fluff/1/HOWTO_RECREATE.txt",
|
|
433
|
+
"spec/data/fluff/1/seq1.fa",
|
|
434
|
+
"spec/data/fluff/1/seq2.fa",
|
|
435
|
+
"spec/data/gapfilling/1/reads.fa",
|
|
436
|
+
"spec/data/gapfilling/1/trail_with_Ns.fa",
|
|
437
|
+
"spec/data/gapfilling/1/velvetAssembly/Graph2",
|
|
438
|
+
"spec/data/gapfilling/1/velvetAssembly/LastGraph",
|
|
439
|
+
"spec/data/gapfilling/1/velvetAssembly/Log",
|
|
440
|
+
"spec/data/gapfilling/1/velvetAssembly/PreGraph",
|
|
441
|
+
"spec/data/gapfilling/1/velvetAssembly/Roadmaps",
|
|
442
|
+
"spec/data/gapfilling/1/velvetAssembly/Sequences",
|
|
443
|
+
"spec/data/gapfilling/1/velvetAssembly/contigs.fa",
|
|
444
|
+
"spec/data/gapfilling/1/velvetAssembly/stats.txt",
|
|
445
|
+
"spec/data/gapfilling/2/HOWTO_recreate",
|
|
446
|
+
"spec/data/gapfilling/2/reference.fa",
|
|
447
|
+
"spec/data/gapfilling/2/reference_part1.fa",
|
|
448
|
+
"spec/data/gapfilling/2/reference_part2.fa",
|
|
449
|
+
"spec/data/gapfilling/2/sammy_reads.fa.gz",
|
|
450
|
+
"spec/data/gapfilling/2/with_gaps.fa",
|
|
451
|
+
"spec/data/gapfilling/3/HOWTO_recreate",
|
|
452
|
+
"spec/data/gapfilling/3/reads.fa.gz",
|
|
453
|
+
"spec/data/gapfilling/3/reference_part1.fa",
|
|
454
|
+
"spec/data/gapfilling/3/reference_part2.fa",
|
|
455
|
+
"spec/data/gapfilling/3/with_gaps.fa",
|
|
456
|
+
"spec/data/gapfilling/4/HOWTO_recreate",
|
|
457
|
+
"spec/data/gapfilling/4/reads.fa.gz",
|
|
458
|
+
"spec/data/gapfilling/5/HOWTO_RECREATE",
|
|
459
|
+
"spec/data/gapfilling/5/answer.fna",
|
|
460
|
+
"spec/data/gapfilling/5/gappy.fna",
|
|
461
|
+
"spec/data/gapfilling/5/reads.fa",
|
|
462
|
+
"spec/data/gapfilling/5/velvet51_3.5/LastGraph",
|
|
463
|
+
"spec/data/gapfilling/5/velvet51_3.5/Sequences",
|
|
464
|
+
"spec/data/gapfilling/6/random1.fa",
|
|
465
|
+
"spec/data/gapfilling/6/random2.fa",
|
|
466
|
+
"spec/data/gapfilling/6/random_sequence_length_2000",
|
|
467
|
+
"spec/data/gapfilling/6/reads.random1.fa.gz",
|
|
468
|
+
"spec/data/gapfilling/6/reads.random2.fa.gz",
|
|
469
|
+
"spec/data/gapfilling/6/to_gapfill.fa",
|
|
470
|
+
"spec/data/kmer_profile_to_assembly/multiple_abundance_file1.csv",
|
|
471
|
+
"spec/data/kmers_count1.csv",
|
|
472
|
+
"spec/data/kmers_count2.csv",
|
|
473
|
+
"spec/data/out",
|
|
474
|
+
"spec/data/positive_latching_pair.fa",
|
|
475
|
+
"spec/data/primers.csv",
|
|
476
|
+
"spec/data/read_selection_by_kmer/blacklist1.txt",
|
|
477
|
+
"spec/data/read_selection_by_kmer/input.fasta",
|
|
478
|
+
"spec/data/read_selection_by_kmer/whitelist1.txt",
|
|
479
|
+
"spec/data/read_selection_by_kmer/whitelist2.txt",
|
|
480
|
+
"spec/data/read_to_node/1_a_graph/HOWTO_RECREATE.txt",
|
|
481
|
+
"spec/data/read_to_node/1_a_graph/LastGraph",
|
|
482
|
+
"spec/data/read_to_node/1_a_graph/ReadToNode.bin",
|
|
483
|
+
"spec/data/read_to_node/2_no_read256_or_259/HOWTO_RECREATE.txt",
|
|
484
|
+
"spec/data/read_to_node/2_no_read256_or_259/LastGraph",
|
|
485
|
+
"spec/data/read_to_node/2_no_read256_or_259/ReadToNode.bin",
|
|
486
|
+
"spec/data/read_to_node/3_no_last_read/LastGraph",
|
|
487
|
+
"spec/data/read_to_node/3_no_last_read/ReadToNode.bin",
|
|
488
|
+
"spec/data/t/details.txt",
|
|
489
|
+
"spec/data/t/details.txt.srt",
|
|
490
|
+
"spec/data/t/location.txt",
|
|
491
|
+
"spec/data/t/location.txt.srt",
|
|
492
|
+
"spec/data/tweak/1_gap_then_unscaffolded/answer.fa",
|
|
493
|
+
"spec/data/tweak/1_gap_then_unscaffolded/reads.fa.gz",
|
|
494
|
+
"spec/data/tweak/1_gap_then_unscaffolded/scaffolds.fa",
|
|
495
|
+
"spec/data/tweak/2_second_genome/answer2.fa",
|
|
496
|
+
"spec/data/tweak/2_second_genome/reads.fa.gz",
|
|
497
|
+
"spec/data/tweak/3_variant/answer.fa",
|
|
498
|
+
"spec/data/tweak/3_variant/lesser_answer.fa",
|
|
499
|
+
"spec/data/tweak/3_variant/reads.fa.gz",
|
|
500
|
+
"spec/data/tweak/3_variant/with_gaps.fa",
|
|
501
|
+
"spec/data/velvet_test_trails/Assem/Graph",
|
|
502
|
+
"spec/data/velvet_test_trails/Assem/Graph2",
|
|
503
|
+
"spec/data/velvet_test_trails/Assem/LastGraph",
|
|
504
|
+
"spec/data/velvet_test_trails/Assem/Log",
|
|
505
|
+
"spec/data/velvet_test_trails/Assem/PreGraph",
|
|
506
|
+
"spec/data/velvet_test_trails/Assem/Roadmaps",
|
|
507
|
+
"spec/data/velvet_test_trails/Assem/Sequences",
|
|
508
|
+
"spec/data/velvet_test_trails/Assem/a.svg",
|
|
509
|
+
"spec/data/velvet_test_trails/Assem/contigs.fa",
|
|
510
|
+
"spec/data/velvet_test_trails/Assem/stats.txt",
|
|
511
|
+
"spec/data/velvet_test_trails/node_fwds.fa",
|
|
512
|
+
"spec/data/velvet_test_trails/node_seqs.fa",
|
|
513
|
+
"spec/data/velvet_test_trails/nodes_fwd_rev.fa",
|
|
514
|
+
"spec/data/velvet_test_trails/read1.fa",
|
|
515
|
+
"spec/data/velvet_test_trails/reads.fa",
|
|
516
|
+
"spec/data/velvet_test_trails_reverse/Assem/LastGraph",
|
|
517
|
+
"spec/data/velvet_test_trails_reverse/Assem/a.svg",
|
|
518
|
+
"spec/data/velvet_test_trails_reverse/reads_reversed.fa",
|
|
519
|
+
"spec/data/visualise/1/LastGraph",
|
|
520
|
+
"spec/data/visualise/2_paired_end/HOWTO_RECREATE.txt",
|
|
521
|
+
"spec/data/visualise/2_paired_end/rand1.fa",
|
|
522
|
+
"spec/data/visualise/2_paired_end/rand2.fa",
|
|
523
|
+
"spec/data/visualise/2_paired_end/with_gaps.fa",
|
|
524
|
+
"spec/data/visualise/2_paired_end/with_gaps.read_pairs.fa.gz",
|
|
525
|
+
"spec/data/wander/1/random1.fa",
|
|
526
|
+
"spec/data/wander/1/random1.sammy.fa",
|
|
527
|
+
"spec/depth_first_search_spec.rb",
|
|
528
|
+
"spec/dijkstra_spec.rb",
|
|
529
|
+
"spec/explore_spec.rb",
|
|
530
|
+
"spec/fluffer_spec.rb",
|
|
531
|
+
"spec/gapfiller_spec.rb",
|
|
532
|
+
"spec/graph_explorer_spec.rb",
|
|
533
|
+
"spec/graph_generator_spec.rb",
|
|
534
|
+
"spec/height_finder_spec.rb",
|
|
535
|
+
"spec/kmer_abundance_pattern_spec.rb",
|
|
536
|
+
"spec/kmer_coverage_based_path_filter_spec.rb",
|
|
537
|
+
"spec/kmer_profile_finder_spec.rb",
|
|
538
|
+
"spec/kmers_count_tabulate_spec.rb",
|
|
539
|
+
"spec/oriented_node_trail_spec.rb",
|
|
540
|
+
"spec/paired_end_neighbours_spec.rb",
|
|
541
|
+
"spec/paths_between_nodes_spec.rb",
|
|
542
|
+
"spec/priner_spec.rb",
|
|
543
|
+
"spec/read_input_spec.rb",
|
|
544
|
+
"spec/read_selection_by_kmer_spec.rb",
|
|
545
|
+
"spec/read_to_node_spec.rb",
|
|
546
|
+
"spec/roundup_spec.rb",
|
|
547
|
+
"spec/scaffold_breaker_spec.rb",
|
|
548
|
+
"spec/sequence_spec.rb",
|
|
549
|
+
"spec/single_coherent_paths_between_nodes_spec.rb",
|
|
550
|
+
"spec/single_coherent_wanderer_spec.rb",
|
|
551
|
+
"spec/single_ended_assembler_spec.rb",
|
|
552
|
+
"spec/spec_helper.rb",
|
|
553
|
+
"spec/velvet_graph_sequence_extractor_spec.rb",
|
|
554
|
+
"spec/visualise_spec.rb",
|
|
555
|
+
"spec/wander_spec.rb",
|
|
556
|
+
"spec/watch_for_changes.sh",
|
|
557
|
+
"validation/fasta_compare.rb",
|
|
558
|
+
"validation/gapfill_simulate_perfect.rb"
|
|
559
|
+
]
|
|
560
|
+
s.homepage = "http://github.com/wwood/finishm"
|
|
561
|
+
s.licenses = ["GPL"]
|
|
562
|
+
s.rubygems_version = "2.2.2"
|
|
563
|
+
s.summary = "Genome improvement and finishing with or without further sequencing effort"
|
|
564
|
+
|
|
565
|
+
if s.respond_to? :specification_version then
|
|
566
|
+
s.specification_version = 4
|
|
567
|
+
|
|
568
|
+
if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
|
|
569
|
+
s.add_runtime_dependency(%q<bio-ipcress>, ["~> 0.0"])
|
|
570
|
+
s.add_runtime_dependency(%q<bio-logger>, ["~> 1.0"])
|
|
571
|
+
s.add_runtime_dependency(%q<bio>, [">= 1.4.3", "~> 1.4"])
|
|
572
|
+
s.add_runtime_dependency(%q<progressbar>, ["~> 0.21"])
|
|
573
|
+
s.add_runtime_dependency(%q<bio-samtools>, ["~> 0.6"])
|
|
574
|
+
s.add_runtime_dependency(%q<ruby-graphviz>, [">= 1.0.9", "~> 1.0"])
|
|
575
|
+
s.add_runtime_dependency(%q<ds>, [">= 0.0.4", "~> 0.0"])
|
|
576
|
+
s.add_runtime_dependency(%q<hopcsv>, [">= 0.4.3", "~> 0.4"])
|
|
577
|
+
s.add_runtime_dependency(%q<bio-velvet>, ["~> 0.6"])
|
|
578
|
+
s.add_runtime_dependency(%q<bio-velvet_underground>, ["~> 0.3"])
|
|
579
|
+
s.add_runtime_dependency(%q<ruby-progressbar>, [">= 1.4.2", "~> 1.4"])
|
|
580
|
+
s.add_runtime_dependency(%q<yargraph>, [">= 0.0.4", "~> 0.0"])
|
|
581
|
+
s.add_runtime_dependency(%q<pry>, ["~> 0.10"])
|
|
582
|
+
s.add_development_dependency(%q<rspec>, [">= 2.8.0", "~> 2.8"])
|
|
583
|
+
s.add_development_dependency(%q<yard>, ["~> 0.7"])
|
|
584
|
+
s.add_development_dependency(%q<rdoc>, ["~> 3.12"])
|
|
585
|
+
s.add_development_dependency(%q<bundler>, [">= 1.6.2", "~> 1.6"])
|
|
586
|
+
s.add_development_dependency(%q<jeweler>, [">= 2.0.1", "~> 2.0"])
|
|
587
|
+
s.add_development_dependency(%q<bio-commandeer>, ["~> 0.1"])
|
|
588
|
+
else
|
|
589
|
+
s.add_dependency(%q<bio-ipcress>, ["~> 0.0"])
|
|
590
|
+
s.add_dependency(%q<bio-logger>, ["~> 1.0"])
|
|
591
|
+
s.add_dependency(%q<bio>, [">= 1.4.3", "~> 1.4"])
|
|
592
|
+
s.add_dependency(%q<progressbar>, ["~> 0.21"])
|
|
593
|
+
s.add_dependency(%q<bio-samtools>, ["~> 0.6"])
|
|
594
|
+
s.add_dependency(%q<ruby-graphviz>, [">= 1.0.9", "~> 1.0"])
|
|
595
|
+
s.add_dependency(%q<ds>, [">= 0.0.4", "~> 0.0"])
|
|
596
|
+
s.add_dependency(%q<hopcsv>, [">= 0.4.3", "~> 0.4"])
|
|
597
|
+
s.add_dependency(%q<bio-velvet>, ["~> 0.6"])
|
|
598
|
+
s.add_dependency(%q<bio-velvet_underground>, ["~> 0.3"])
|
|
599
|
+
s.add_dependency(%q<ruby-progressbar>, [">= 1.4.2", "~> 1.4"])
|
|
600
|
+
s.add_dependency(%q<yargraph>, [">= 0.0.4", "~> 0.0"])
|
|
601
|
+
s.add_dependency(%q<pry>, ["~> 0.10"])
|
|
602
|
+
s.add_dependency(%q<rspec>, [">= 2.8.0", "~> 2.8"])
|
|
603
|
+
s.add_dependency(%q<yard>, ["~> 0.7"])
|
|
604
|
+
s.add_dependency(%q<rdoc>, ["~> 3.12"])
|
|
605
|
+
s.add_dependency(%q<bundler>, [">= 1.6.2", "~> 1.6"])
|
|
606
|
+
s.add_dependency(%q<jeweler>, [">= 2.0.1", "~> 2.0"])
|
|
607
|
+
s.add_dependency(%q<bio-commandeer>, ["~> 0.1"])
|
|
608
|
+
end
|
|
609
|
+
else
|
|
610
|
+
s.add_dependency(%q<bio-ipcress>, ["~> 0.0"])
|
|
611
|
+
s.add_dependency(%q<bio-logger>, ["~> 1.0"])
|
|
612
|
+
s.add_dependency(%q<bio>, [">= 1.4.3", "~> 1.4"])
|
|
613
|
+
s.add_dependency(%q<progressbar>, ["~> 0.21"])
|
|
614
|
+
s.add_dependency(%q<bio-samtools>, ["~> 0.6"])
|
|
615
|
+
s.add_dependency(%q<ruby-graphviz>, [">= 1.0.9", "~> 1.0"])
|
|
616
|
+
s.add_dependency(%q<ds>, [">= 0.0.4", "~> 0.0"])
|
|
617
|
+
s.add_dependency(%q<hopcsv>, [">= 0.4.3", "~> 0.4"])
|
|
618
|
+
s.add_dependency(%q<bio-velvet>, ["~> 0.6"])
|
|
619
|
+
s.add_dependency(%q<bio-velvet_underground>, ["~> 0.3"])
|
|
620
|
+
s.add_dependency(%q<ruby-progressbar>, [">= 1.4.2", "~> 1.4"])
|
|
621
|
+
s.add_dependency(%q<yargraph>, [">= 0.0.4", "~> 0.0"])
|
|
622
|
+
s.add_dependency(%q<pry>, ["~> 0.10"])
|
|
623
|
+
s.add_dependency(%q<rspec>, [">= 2.8.0", "~> 2.8"])
|
|
624
|
+
s.add_dependency(%q<yard>, ["~> 0.7"])
|
|
625
|
+
s.add_dependency(%q<rdoc>, ["~> 3.12"])
|
|
626
|
+
s.add_dependency(%q<bundler>, [">= 1.6.2", "~> 1.6"])
|
|
627
|
+
s.add_dependency(%q<jeweler>, [">= 2.0.1", "~> 2.0"])
|
|
628
|
+
s.add_dependency(%q<bio-commandeer>, ["~> 0.1"])
|
|
629
|
+
end
|
|
630
|
+
end
|
|
631
|
+
|