bio-velvet_underground 0.0.1

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Files changed (286) hide show
  1. checksums.yaml +7 -0
  2. data/.document +5 -0
  3. data/.gitmodules +3 -0
  4. data/.travis.yml +13 -0
  5. data/Gemfile +19 -0
  6. data/LICENSE.txt +20 -0
  7. data/README.md +53 -0
  8. data/Rakefile +51 -0
  9. data/VERSION +1 -0
  10. data/ext/bioruby.patch +60 -0
  11. data/ext/mkrf_conf.rb +50 -0
  12. data/ext/src/Makefile +125 -0
  13. data/ext/src/src/allocArray.c +305 -0
  14. data/ext/src/src/allocArray.h +86 -0
  15. data/ext/src/src/autoOpen.c +107 -0
  16. data/ext/src/src/autoOpen.h +18 -0
  17. data/ext/src/src/binarySequences.c +813 -0
  18. data/ext/src/src/binarySequences.h +125 -0
  19. data/ext/src/src/concatenatedGraph.c +233 -0
  20. data/ext/src/src/concatenatedGraph.h +30 -0
  21. data/ext/src/src/concatenatedPreGraph.c +262 -0
  22. data/ext/src/src/concatenatedPreGraph.h +29 -0
  23. data/ext/src/src/correctedGraph.c +2642 -0
  24. data/ext/src/src/correctedGraph.h +32 -0
  25. data/ext/src/src/dfib.c +509 -0
  26. data/ext/src/src/dfib.h +69 -0
  27. data/ext/src/src/dfibHeap.c +89 -0
  28. data/ext/src/src/dfibHeap.h +39 -0
  29. data/ext/src/src/dfibpriv.h +105 -0
  30. data/ext/src/src/fib.c +628 -0
  31. data/ext/src/src/fib.h +78 -0
  32. data/ext/src/src/fibHeap.c +79 -0
  33. data/ext/src/src/fibHeap.h +41 -0
  34. data/ext/src/src/fibpriv.h +110 -0
  35. data/ext/src/src/globals.h +153 -0
  36. data/ext/src/src/graph.c +3983 -0
  37. data/ext/src/src/graph.h +233 -0
  38. data/ext/src/src/graphReConstruction.c +1472 -0
  39. data/ext/src/src/graphReConstruction.h +30 -0
  40. data/ext/src/src/graphStats.c +2167 -0
  41. data/ext/src/src/graphStats.h +72 -0
  42. data/ext/src/src/kmer.c +652 -0
  43. data/ext/src/src/kmer.h +73 -0
  44. data/ext/src/src/kmerOccurenceTable.c +236 -0
  45. data/ext/src/src/kmerOccurenceTable.h +44 -0
  46. data/ext/src/src/kseq.h +223 -0
  47. data/ext/src/src/locallyCorrectedGraph.c +557 -0
  48. data/ext/src/src/locallyCorrectedGraph.h +40 -0
  49. data/ext/src/src/passageMarker.c +677 -0
  50. data/ext/src/src/passageMarker.h +137 -0
  51. data/ext/src/src/preGraph.c +1717 -0
  52. data/ext/src/src/preGraph.h +106 -0
  53. data/ext/src/src/preGraphConstruction.c +990 -0
  54. data/ext/src/src/preGraphConstruction.h +26 -0
  55. data/ext/src/src/readCoherentGraph.c +557 -0
  56. data/ext/src/src/readCoherentGraph.h +30 -0
  57. data/ext/src/src/readSet.c +1734 -0
  58. data/ext/src/src/readSet.h +67 -0
  59. data/ext/src/src/recycleBin.c +199 -0
  60. data/ext/src/src/recycleBin.h +58 -0
  61. data/ext/src/src/roadMap.c +342 -0
  62. data/ext/src/src/roadMap.h +65 -0
  63. data/ext/src/src/run.c +318 -0
  64. data/ext/src/src/run.h +52 -0
  65. data/ext/src/src/run2.c +712 -0
  66. data/ext/src/src/scaffold.c +1876 -0
  67. data/ext/src/src/scaffold.h +64 -0
  68. data/ext/src/src/shortReadPairs.c +1243 -0
  69. data/ext/src/src/shortReadPairs.h +32 -0
  70. data/ext/src/src/splay.c +259 -0
  71. data/ext/src/src/splay.h +43 -0
  72. data/ext/src/src/splayTable.c +1315 -0
  73. data/ext/src/src/splayTable.h +31 -0
  74. data/ext/src/src/tightString.c +362 -0
  75. data/ext/src/src/tightString.h +82 -0
  76. data/ext/src/src/utility.c +199 -0
  77. data/ext/src/src/utility.h +98 -0
  78. data/ext/src/third-party/zlib-1.2.3/ChangeLog +855 -0
  79. data/ext/src/third-party/zlib-1.2.3/FAQ +339 -0
  80. data/ext/src/third-party/zlib-1.2.3/INDEX +51 -0
  81. data/ext/src/third-party/zlib-1.2.3/Makefile +154 -0
  82. data/ext/src/third-party/zlib-1.2.3/Makefile.in +154 -0
  83. data/ext/src/third-party/zlib-1.2.3/README +125 -0
  84. data/ext/src/third-party/zlib-1.2.3/adler32.c +149 -0
  85. data/ext/src/third-party/zlib-1.2.3/algorithm.txt +209 -0
  86. data/ext/src/third-party/zlib-1.2.3/amiga/Makefile.pup +66 -0
  87. data/ext/src/third-party/zlib-1.2.3/amiga/Makefile.sas +65 -0
  88. data/ext/src/third-party/zlib-1.2.3/as400/bndsrc +132 -0
  89. data/ext/src/third-party/zlib-1.2.3/as400/compile.clp +123 -0
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  92. data/ext/src/third-party/zlib-1.2.3/compress.c +79 -0
  93. data/ext/src/third-party/zlib-1.2.3/configure +459 -0
  94. data/ext/src/third-party/zlib-1.2.3/contrib/README.contrib +71 -0
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  107. data/ext/src/third-party/zlib-1.2.3/contrib/asm586/README.586 +43 -0
  108. data/ext/src/third-party/zlib-1.2.3/contrib/asm586/match.S +364 -0
  109. data/ext/src/third-party/zlib-1.2.3/contrib/asm686/README.686 +34 -0
  110. data/ext/src/third-party/zlib-1.2.3/contrib/asm686/match.S +329 -0
  111. data/ext/src/third-party/zlib-1.2.3/contrib/blast/Makefile +8 -0
  112. data/ext/src/third-party/zlib-1.2.3/contrib/blast/README +4 -0
  113. data/ext/src/third-party/zlib-1.2.3/contrib/blast/blast.c +444 -0
  114. data/ext/src/third-party/zlib-1.2.3/contrib/blast/blast.h +71 -0
  115. data/ext/src/third-party/zlib-1.2.3/contrib/blast/test.pk +0 -0
  116. data/ext/src/third-party/zlib-1.2.3/contrib/blast/test.txt +1 -0
  117. data/ext/src/third-party/zlib-1.2.3/contrib/delphi/ZLib.pas +557 -0
  118. data/ext/src/third-party/zlib-1.2.3/contrib/delphi/ZLibConst.pas +11 -0
  119. data/ext/src/third-party/zlib-1.2.3/contrib/delphi/readme.txt +76 -0
  120. data/ext/src/third-party/zlib-1.2.3/contrib/delphi/zlibd32.mak +93 -0
  121. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib.build +33 -0
  122. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib.chm +0 -0
  123. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib.sln +21 -0
  124. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/AssemblyInfo.cs +58 -0
  125. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/ChecksumImpl.cs +202 -0
  126. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/CircularBuffer.cs +83 -0
  127. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/CodecBase.cs +198 -0
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  129. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/DotZLib.cs +288 -0
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  131. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/GZipStream.cs +301 -0
  132. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/Inflater.cs +105 -0
  133. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/UnitTests.cs +274 -0
  134. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/LICENSE_1_0.txt +23 -0
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  136. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/README +1 -0
  137. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/infback9.c +608 -0
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  141. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/inftree9.c +323 -0
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  145. data/ext/src/third-party/zlib-1.2.3/contrib/iostream/test.cpp +24 -0
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  250. data/ext/src/third-party/zlib-1.2.3/old/README +3 -0
  251. data/ext/src/third-party/zlib-1.2.3/old/descrip.mms +48 -0
  252. data/ext/src/third-party/zlib-1.2.3/old/os2/Makefile.os2 +136 -0
  253. data/ext/src/third-party/zlib-1.2.3/old/os2/zlib.def +51 -0
  254. data/ext/src/third-party/zlib-1.2.3/old/visual-basic.txt +160 -0
  255. data/ext/src/third-party/zlib-1.2.3/old/zlib.html +971 -0
  256. data/ext/src/third-party/zlib-1.2.3/projects/README.projects +41 -0
  257. data/ext/src/third-party/zlib-1.2.3/projects/visualc6/README.txt +73 -0
  258. data/ext/src/third-party/zlib-1.2.3/projects/visualc6/example.dsp +278 -0
  259. data/ext/src/third-party/zlib-1.2.3/projects/visualc6/minigzip.dsp +278 -0
  260. data/ext/src/third-party/zlib-1.2.3/projects/visualc6/zlib.dsp +609 -0
  261. data/ext/src/third-party/zlib-1.2.3/projects/visualc6/zlib.dsw +59 -0
  262. data/ext/src/third-party/zlib-1.2.3/qnx/package.qpg +141 -0
  263. data/ext/src/third-party/zlib-1.2.3/trees.c +1219 -0
  264. data/ext/src/third-party/zlib-1.2.3/trees.h +128 -0
  265. data/ext/src/third-party/zlib-1.2.3/uncompr.c +61 -0
  266. data/ext/src/third-party/zlib-1.2.3/win32/DLL_FAQ.txt +397 -0
  267. data/ext/src/third-party/zlib-1.2.3/win32/Makefile.bor +107 -0
  268. data/ext/src/third-party/zlib-1.2.3/win32/Makefile.emx +69 -0
  269. data/ext/src/third-party/zlib-1.2.3/win32/Makefile.gcc +141 -0
  270. data/ext/src/third-party/zlib-1.2.3/win32/Makefile.msc +126 -0
  271. data/ext/src/third-party/zlib-1.2.3/win32/VisualC.txt +3 -0
  272. data/ext/src/third-party/zlib-1.2.3/win32/zlib.def +60 -0
  273. data/ext/src/third-party/zlib-1.2.3/win32/zlib1.rc +39 -0
  274. data/ext/src/third-party/zlib-1.2.3/zconf.h +332 -0
  275. data/ext/src/third-party/zlib-1.2.3/zconf.in.h +332 -0
  276. data/ext/src/third-party/zlib-1.2.3/zlib.3 +159 -0
  277. data/ext/src/third-party/zlib-1.2.3/zlib.h +1357 -0
  278. data/ext/src/third-party/zlib-1.2.3/zutil.c +318 -0
  279. data/ext/src/third-party/zlib-1.2.3/zutil.h +269 -0
  280. data/lib/bio-velvet_underground.rb +12 -0
  281. data/lib/bio-velvet_underground/external/VERSION +1 -0
  282. data/lib/bio-velvet_underground/velvet_underground.rb +72 -0
  283. data/spec/binary_sequence_store_spec.rb +27 -0
  284. data/spec/data/1/CnyUnifiedSeq +0 -0
  285. data/spec/spec_helper.rb +31 -0
  286. metadata +456 -0
@@ -0,0 +1,41 @@
1
+ This directory contains project files for building zlib under various
2
+ Integrated Development Environments (IDE).
3
+
4
+ If you wish to submit a new project to this directory, you should comply
5
+ to the following requirements. Otherwise (e.g. if you wish to integrate
6
+ a custom piece of code that changes the zlib interface or its behavior),
7
+ please consider submitting the project to the contrib directory.
8
+
9
+
10
+ Requirements
11
+ ============
12
+
13
+ - The project must build zlib using the source files from the official
14
+ zlib source distribution, exclusively.
15
+
16
+ - If the project produces redistributable builds (e.g. shared objects
17
+ or DLL files), these builds must be compatible to those produced by
18
+ makefiles, if such makefiles exist in the zlib distribution.
19
+ In particular, if the project produces a DLL build for the Win32
20
+ platform, this build must comply to the officially-ammended Win32 DLL
21
+ Application Binary Interface (ABI), described in win32/DLL_FAQ.txt.
22
+
23
+ - The project may provide additional build targets, which depend on
24
+ 3rd-party (unofficially-supported) software, present in the contrib
25
+ directory. For example, it is possible to provide an "ASM build",
26
+ besides the officially-supported build, and have ASM source files
27
+ among its dependencies.
28
+
29
+ - If there are significant differences between the project files created
30
+ by different versions of an IDE (e.g. Visual C++ 6.0 vs. 7.0), the name
31
+ of the project directory should contain the version number of the IDE
32
+ for which the project is intended (e.g. "visualc6" for Visual C++ 6.0,
33
+ or "visualc7" for Visual C++ 7.0 and 7.1).
34
+
35
+
36
+ Current projects
37
+ ================
38
+
39
+ visualc6/ by Simon-Pierre Cadieux <methodex@methodex.ca>
40
+ and Cosmin Truta <cosmint@cs.ubbcluj.ro>
41
+ Project for Microsoft Visual C++ 6.0
@@ -0,0 +1,73 @@
1
+ Microsoft Developer Studio Project Files, Format Version 6.00 for zlib.
2
+
3
+ Copyright (C) 2000-2004 Simon-Pierre Cadieux.
4
+ Copyright (C) 2004 Cosmin Truta.
5
+ For conditions of distribution and use, see copyright notice in zlib.h.
6
+
7
+
8
+ This project builds the zlib binaries as follows:
9
+
10
+ * Win32_DLL_Release\zlib1.dll DLL build
11
+ * Win32_DLL_Debug\zlib1d.dll DLL build (debug version)
12
+ * Win32_DLL_ASM_Release\zlib1.dll DLL build using ASM code
13
+ * Win32_DLL_ASM_Debug\zlib1d.dll DLL build using ASM code (debug version)
14
+ * Win32_LIB_Release\zlib.lib static build
15
+ * Win32_LIB_Debug\zlibd.lib static build (debug version)
16
+ * Win32_LIB_ASM_Release\zlib.lib static build using ASM code
17
+ * Win32_LIB_ASM_Debug\zlibd.lib static build using ASM code (debug version)
18
+
19
+
20
+ For more information regarding the DLL builds, please see the DLL FAQ
21
+ in ..\..\win32\DLL_FAQ.txt.
22
+
23
+
24
+ To build and test:
25
+
26
+ 1) On the main menu, select "File | Open Workspace".
27
+ Open "zlib.dsw".
28
+
29
+ 2) Select "Build | Set Active Configuration".
30
+ Choose the configuration you wish to build.
31
+
32
+ 3) Select "Build | Clean".
33
+
34
+ 4) Select "Build | Build ... (F7)". Ignore warning messages about
35
+ not being able to find certain include files (e.g. alloc.h).
36
+
37
+ 5) If you built one of the sample programs (example or minigzip),
38
+ select "Build | Execute ... (Ctrl+F5)".
39
+
40
+
41
+ To use:
42
+
43
+ 1) Select "Project | Settings (Alt+F7)".
44
+ Make note of the configuration names used in your project.
45
+ Usually, these names are "Win32 Release" and "Win32 Debug".
46
+
47
+ 2) In the Workspace window, select the "FileView" tab.
48
+ Right-click on the root item "Workspace '...'".
49
+ Select "Insert Project into Workspace".
50
+ Switch on the checkbox "Dependency of:", and select the name
51
+ of your project. Open "zlib.dsp".
52
+
53
+ 3) Select "Build | Configurations".
54
+ For each configuration of your project:
55
+ 3.1) Choose the zlib configuration you wish to use.
56
+ 3.2) Click on "Add".
57
+ 3.3) Set the new zlib configuration name to the name used by
58
+ the configuration from the current iteration.
59
+
60
+ 4) Select "Build | Set Active Configuration".
61
+ Choose the configuration you wish to build.
62
+
63
+ 5) Select "Build | Build ... (F7)".
64
+
65
+ 6) If you built an executable program, select
66
+ "Build | Execute ... (Ctrl+F5)".
67
+
68
+
69
+ Note:
70
+
71
+ To build the ASM-enabled code, you need Microsoft Assembler
72
+ (ML.EXE). You can get it by downloading and installing the
73
+ latest Processor Pack for Visual C++ 6.0.
@@ -0,0 +1,278 @@
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+ !MESSAGE "example - Win32 DLL ASM Debug" (based on "Win32 (x86) Console Application")
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+ !MESSAGE "example - Win32 LIB Release" (based on "Win32 (x86) Console Application")
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+ !MESSAGE "example - Win32 LIB Debug" (based on "Win32 (x86) Console Application")
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+ !MESSAGE "example - Win32 LIB ASM Release" (based on "Win32 (x86) Console Application")
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+ !MESSAGE "example - Win32 LIB ASM Debug" (based on "Win32 (x86) Console Application")
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