scbi_fqbin 0.2.2 → 0.2.3

Sign up to get free protection for your applications and to get access to all the features.
Files changed (116) hide show
  1. checksums.yaml +7 -0
  2. data/.DS_Store +0 -0
  3. data/.gitignore +14 -0
  4. data/Gemfile +4 -0
  5. data/LICENSE.txt +22 -0
  6. data/{README.rdoc → README.md} +0 -0
  7. data/Rakefile +8 -28
  8. data/lib/scbi_fqbin.rb +3 -5
  9. data/lib/scbi_fqbin/fastabin.rb +411 -0
  10. data/lib/scbi_fqbin/fastq_file_c.rb +373 -0
  11. data/lib/scbi_fqbin/fbin_file.rb +1 -1
  12. data/lib/scbi_fqbin/t.rb +9 -0
  13. data/lib/scbi_fqbin/t2.rb +12 -0
  14. data/lib/scbi_fqbin/version.rb +3 -0
  15. data/lib_fqbin_src.zip +0 -0
  16. data/lib_fqbin_src/Makefile +66 -0
  17. data/lib_fqbin_src/fq +0 -0
  18. data/lib_fqbin_src/fq.c +165 -0
  19. data/lib_fqbin_src/hash_fqbin +0 -0
  20. data/lib_fqbin_src/hash_fqbin.c +212 -0
  21. data/lib_fqbin_src/idx_fqbin +21 -0
  22. data/lib_fqbin_src/iterate_fqbin +0 -0
  23. data/lib_fqbin_src/iterate_fqbin.c +136 -0
  24. data/lib_fqbin_src/lib_fqbin.c +1748 -0
  25. data/lib_fqbin_src/lib_fqbin.h +194 -0
  26. data/lib_fqbin_src/mk_fqbin +0 -0
  27. data/lib_fqbin_src/mk_fqbin.c +138 -0
  28. data/lib_fqbin_src/other/bwxform.c +915 -0
  29. data/lib_fqbin_src/other/bwxform.h +74 -0
  30. data/lib_fqbin_src/other/find_in_index.c +130 -0
  31. data/lib_fqbin_src/other/hash_fbin_nogzchunks.c +164 -0
  32. data/lib_fqbin_src/other/idx_fqbin +0 -0
  33. data/lib_fqbin_src/other/idx_fqbin.c +67 -0
  34. data/lib_fqbin_src/other/make_hsh.sh +14 -0
  35. data/lib_fqbin_src/other/rd_extras_fbin.c +45 -0
  36. data/lib_fqbin_src/read_fq +0 -0
  37. data/lib_fqbin_src/read_fq.c +143 -0
  38. data/lib_fqbin_src/read_fqbin +0 -0
  39. data/lib_fqbin_src/read_fqbin.c +101 -0
  40. data/lib_fqbin_src/sort_index +9 -0
  41. data/lib_fqbin_src/test.rb +13 -0
  42. data/scbi_fqbin.gemspec +25 -0
  43. data/test/build.rake +15 -0
  44. data/test/fbinfile +0 -0
  45. data/test/fbinfile.index +0 -0
  46. data/test/no_test_fill_file.rb +66 -0
  47. data/test/old/app.rb +43 -0
  48. data/test/old/bin/iterate_fastabin.rb +54 -0
  49. data/test/old/bin/mk_fastabin.rb +22 -0
  50. data/test/old/bin/rd_fastabin.rb +36 -0
  51. data/test/old/bin/rd_fq.rb +20 -0
  52. data/test/old/bioruby.rb +27 -0
  53. data/test/old/c/Makefile +34 -0
  54. data/test/old/c/fbin_lib.zip +0 -0
  55. data/test/old/c/iterate_fbin.c +54 -0
  56. data/test/old/c/libreria_gz.c +707 -0
  57. data/test/old/c/libreria_gz.h +127 -0
  58. data/test/old/c/main.c +86 -0
  59. data/test/old/c/mk_fbin.c +24 -0
  60. data/test/old/c/rd_seq_fbin.c +44 -0
  61. data/test/old/c/test_ffi/a.out +0 -0
  62. data/test/old/c/test_ffi/app.c +26 -0
  63. data/test/old/c/test_ffi/app.rb +19 -0
  64. data/test/old/c/test_ffi/liblibreria_gz.dylib +0 -0
  65. data/test/old/c/test_ffi/libmylibrary.dylib +0 -0
  66. data/test/old/c/test_ffi/my_library.rb +23 -0
  67. data/test/old/c/test_ffi/mylibrary.c +22 -0
  68. data/test/old/c/test_ffi/mylibrary.h +6 -0
  69. data/test/old/c/usage_instructions.txt +62 -0
  70. data/test/old/ext/Makefile +187 -0
  71. data/test/old/ext/Makefile.dario +34 -0
  72. data/test/old/ext/extconf.rb +8 -0
  73. data/test/old/ext/mk_fbin.c +24 -0
  74. data/test/old/ext/sample/extras.txt +4 -0
  75. data/{.gemtest → test/old/ext/sample/extras2.txt} +0 -0
  76. data/test/old/ext/sample/f1.fasta +10 -0
  77. data/test/old/ext/sample/f1.fasta.qual +10 -0
  78. data/test/old/ext/sample/f1.fbin +0 -0
  79. data/test/old/ext/sample/f1.fbin.index +0 -0
  80. data/test/old/ext/sample/main.c +86 -0
  81. data/test/old/ext/usage_instructions.txt +62 -0
  82. data/test/old/t_scbi_fastabin.rb +140 -0
  83. data/test/read_tests/10-original_sizes.sh +16 -0
  84. data/test/read_tests/20-fq_time.sh +23 -0
  85. data/test/read_tests/30-fbin_read_time.sh +23 -0
  86. data/test/read_tests/40-bsc_read_time.sh +21 -0
  87. data/test/read_tests/50-fq_time_x4.sh +25 -0
  88. data/test/read_tests/60-fbin_read_time_x4.sh +24 -0
  89. data/test/read_tests/70-bsc_read_time_x4.sh +32 -0
  90. data/test/results_bio_scbi_fasta.txt +11 -0
  91. data/test/{test_scbi_fbin_file.rb → scbi_fbin_file_test.rb} +0 -0
  92. data/test/speed.txt +81 -0
  93. data/test/t_scbi_fasta.rb +12 -0
  94. data/test/write_tests/10-original_sizes.sh +16 -0
  95. data/test/write_tests/20-zip_time.sh +17 -0
  96. data/test/write_tests/30-mk_fbin_time.sh +23 -0
  97. data/test/write_tests/31-mk_fbin_time_f30.sh +21 -0
  98. data/test/write_tests/40-gzip_time.sh +16 -0
  99. data/test/write_tests/41-bsc_time.sh +16 -0
  100. data/test/write_tests/50-zip_sizes.sh +16 -0
  101. data/test/write_tests/60-fbin_sizes.sh +17 -0
  102. data/test/write_tests/61-fbin_sizes_f30.sh +16 -0
  103. data/test/write_tests/70-gzip_sizes.sh +17 -0
  104. data/test/write_tests/80-bsc_sizes.sh +17 -0
  105. data/website/index.html +87 -0
  106. data/website/index.txt +81 -0
  107. data/website/javascripts/rounded_corners_lite.inc.js +285 -0
  108. data/website/stylesheets/screen.css +159 -0
  109. data/website/template.html.erb +50 -0
  110. metadata +208 -95
  111. data/History.txt +0 -19
  112. data/Manifest.txt +0 -12
  113. data/PostInstall.txt +0 -7
  114. data/script/console +0 -10
  115. data/script/destroy +0 -14
  116. data/script/generate +0 -14
data/History.txt DELETED
@@ -1,19 +0,0 @@
1
- === 0.2.2 2013-05-09
2
-
3
- Added extra dependencies
4
-
5
- === 0.2.1 2013-05-09
6
-
7
- * First public release
8
-
9
- === 0.0.1 2010-05-14
10
-
11
- * 1 major enhancement:
12
- * Initial release
13
-
14
- === 0.1.0 2010-05-31
15
-
16
- * 1 major enhancement:
17
- * Added extras to sequences
18
-
19
-
data/Manifest.txt DELETED
@@ -1,12 +0,0 @@
1
- History.txt
2
- Manifest.txt
3
- PostInstall.txt
4
- README.rdoc
5
- Rakefile
6
- script/console
7
- script/destroy
8
- script/generate
9
- lib/scbi_fqbin/fbin_file.rb
10
- lib/scbi_fqbin.rb
11
- test/test_helper.rb
12
- test/test_scbi_fbin_file.rb
data/PostInstall.txt DELETED
@@ -1,7 +0,0 @@
1
-
2
- For more information on scbi_fqbin, see http://scbi_fqbin.rubyforge.org
3
-
4
- NOTE: Change this information in PostInstall.txt
5
- You can also delete it if you don't want it.
6
-
7
-
data/script/console DELETED
@@ -1,10 +0,0 @@
1
- #!/usr/bin/env ruby
2
- # File: script/console
3
- irb = RUBY_PLATFORM =~ /(:?mswin|mingw)/ ? 'irb.bat' : 'irb'
4
-
5
- libs = " -r irb/completion"
6
- # Perhaps use a console_lib to store any extra methods I may want available in the cosole
7
- # libs << " -r #{File.dirname(__FILE__) + '/../lib/console_lib/console_logger.rb'}"
8
- libs << " -r #{File.dirname(__FILE__) + '/../lib/scbi_fqbin.rb'}"
9
- puts "Loading scbi_fqbin gem"
10
- exec "#{irb} #{libs} --simple-prompt"
data/script/destroy DELETED
@@ -1,14 +0,0 @@
1
- #!/usr/bin/env ruby
2
- APP_ROOT = File.expand_path(File.join(File.dirname(__FILE__), '..'))
3
-
4
- begin
5
- require 'rubigen'
6
- rescue LoadError
7
- require 'rubygems'
8
- require 'rubigen'
9
- end
10
- require 'rubigen/scripts/destroy'
11
-
12
- ARGV.shift if ['--help', '-h'].include?(ARGV[0])
13
- RubiGen::Base.use_component_sources! [:rubygems, :newgem, :newgem_theme, :test_unit]
14
- RubiGen::Scripts::Destroy.new.run(ARGV)
data/script/generate DELETED
@@ -1,14 +0,0 @@
1
- #!/usr/bin/env ruby
2
- APP_ROOT = File.expand_path(File.join(File.dirname(__FILE__), '..'))
3
-
4
- begin
5
- require 'rubigen'
6
- rescue LoadError
7
- require 'rubygems'
8
- require 'rubigen'
9
- end
10
- require 'rubigen/scripts/generate'
11
-
12
- ARGV.shift if ['--help', '-h'].include?(ARGV[0])
13
- RubiGen::Base.use_component_sources! [:rubygems, :newgem, :newgem_theme, :test_unit]
14
- RubiGen::Scripts::Generate.new.run(ARGV)