scbi_fqbin 0.2.2 → 0.2.3

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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/website/stylesheets/screen.css ADDED
@@ -0,0 +1,159 @@
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+ body {
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+ background-color: #8DBD82;
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+ font-family: "Georgia", sans-serif;
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+ font-size: 16px;
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+ line-height: 1.6em;
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+ padding: 1.6em 0 0 0;
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+ color: #333;
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+ }
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+ h1, h2, h3, h4, h5, h6 {
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+ color: #444;
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+ }
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+ h1 {
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+ font-family: sans-serif;
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+ font-weight: normal;
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+ font-size: 4em;
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+ line-height: 0.8em;
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+ letter-spacing: -0.1ex;
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+ margin: 5px;
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+ }
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+ li {
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+ padding: 0;
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+ margin: 0;
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+ list-style-type: square;
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+ }
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+ a {
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+ color: #5E5AFF;
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+ background-color: #A1DDB1;
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+ font-weight: normal;
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+ text-decoration: underline;
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+ }
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+ blockquote {
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+ font-size: 90%;
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+ font-style: italic;
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+ border-left: 1px solid #111;
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+ padding-left: 1em;
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+ }
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+ .caps {
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+ font-size: 80%;
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+ }
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+
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+ #main {
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+ width: 55em;
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+ padding: 0;
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+ margin: 0 auto;
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+ }
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+ .coda {
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+ text-align: right;
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+ color: #77f;
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+ font-size: smaller;
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+ }
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+
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+ table {
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+ font-size: 90%;
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+ line-height: 1.4em;
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+ color: #ff8;
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+ background-color: #111;
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+ padding: 2px 10px 2px 10px;
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+ border-style: dashed;
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+ }
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+
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+ th {
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+ color: #fff;
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+ }
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+
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+ td {
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+ padding: 2px 10px 2px 10px;
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+ }
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+
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+ .success {
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+ color: #0CC52B;
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+ }
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+
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+ .failed {
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+ color: #E90A1B;
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+ }
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+
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+ .unknown {
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+ color: #995000;
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+ }
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+ pre, code {
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+ font-family: monospace;
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+ font-size: 90%;
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+ line-height: 1.4em;
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+ color: #ff8;
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+ background-color: #111;
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+ width: 40em;
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+ padding: 2px 10px 2px 10px;
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+ }
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+ .comment { color: #aaa; font-style: italic; }
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+ .keyword { color: #eff; font-weight: bold; }
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+ .punct { color: #eee; font-weight: bold; }
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+ .symbol { color: #0bb; }
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+ .string { color: #6b4; }
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+ .ident { color: #ff8; }
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+ .constant { color: #66f; }
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+ .regex { color: #ec6; }
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+ .number { color: #F99; }
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+ .expr { color: #227; }
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+
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+ .sidebar {
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+ float: right;
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+ }
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+
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+ #version {
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+ width: 217px;
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+ text-align: right;
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+ font-family: sans-serif;
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+ font-weight: normal;
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+ color: #141331;
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+ padding: 15px 20px 10px 20px;
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+ margin: 0 auto;
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+ margin-top: 15px;
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+ background-color: #9A5535;
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+ border: 3px solid #7E393E;
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+ }
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+
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+ #version .numbers {
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+ display: block;
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+ font-size: 4em;
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+ line-height: 0.8em;
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+ letter-spacing: -0.1ex;
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+ margin-bottom: 15px;
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+ }
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+
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+ #version p {
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+ text-decoration: none;
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+ color: #F1F4FF;
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+ background-color: #9A5535;
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+ margin: 0;
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+ padding: 0;
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+ }
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+
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+ #version a {
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+ text-decoration: none;
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+ color: #F1F4FF;
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+ background-color: #9A5535;
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+ }
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+
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+ .clickable {
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+ cursor: pointer;
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+ cursor: hand;
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+ }
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+
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+ #twitter_search {
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+ margin: 40px 0 10px 15px;
146
+ color: #F1F4FF;
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+ background-color: #9A5535;
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+ border: 3px solid #7E393E;
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+ }
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+
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+ #twitter_search h3 {
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+ color: #F1F4FF;
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+ margin-bottom: 0px;
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+ }
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+
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+ #twitter_search center b {
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+ display: none;
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+ }
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+
data/website/template.html.erb ADDED
@@ -0,0 +1,50 @@
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+ <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
3
+ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
4
+ <head>
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+ <link rel="stylesheet" href="stylesheets/screen.css" type="text/css" media="screen" />
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+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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+ <title>
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+ <%= title %>
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+ </title>
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+ <script src="javascripts/rounded_corners_lite.inc.js" type="text/javascript"></script>
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+ <style>
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+
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+ </style>
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+ <script type="text/javascript">
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+ window.onload = function() {
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+ settings = {
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+ tl: { radius: 10 },
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+ tr: { radius: 10 },
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+ bl: { radius: 10 },
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+ br: { radius: 10 },
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+ antiAlias: true,
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+ autoPad: true,
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+ validTags: ["div"]
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+ }
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+ var versionBox = new curvyCorners(settings, document.getElementById("version"));
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+ versionBox.applyCornersToAll();
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+ }
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+ </script>
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+ </head>
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+ <body>
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+ <div id="main">
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+
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+ <h1><%= title %></h1>
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+ <div class="sidebar">
35
+ <div id="version" class="clickable" onclick='document.location = "<%= download %>"; return false'>
36
+ <p>Get Version</p>
37
+ <a href="<%= download %>" class="numbers"><%= version %></a>
38
+ </div>
39
+ </div>
40
+ <%= body %>
41
+ <p class="coda">
42
+ <a href="FIXME email">FIXME full name</a>, <%= modified.pretty %><br>
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+ Theme extended from <a href="http://rb2js.rubyforge.org/">Paul Battley</a>
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+ </p>
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+ </div>
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+
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+ <!-- insert site tracking codes here, like Google Urchin -->
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+
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+ </body>
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+ </html>
metadata CHANGED
@@ -1,153 +1,266 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: scbi_fqbin
3
3
  version: !ruby/object:Gem::Version
4
- version: 0.2.2
5
- prerelease:
4
+ version: 0.2.3
6
5
  platform: ruby
7
6
  authors:
8
- - Dario Guerrero
7
+ - dariogf
9
8
  autorequire:
10
9
  bindir: bin
11
10
  cert_chain: []
12
- date: 2013-05-09 00:00:00.000000000 Z
11
+ date: 2014-12-03 00:00:00.000000000 Z
13
12
  dependencies:
14
- - !ruby/object:Gem::Dependency
15
- name: scbi_fasta
16
- requirement: !ruby/object:Gem::Requirement
17
- none: false
18
- requirements:
19
- - - ! '>='
20
- - !ruby/object:Gem::Version
21
- version: 0.0.1
22
- type: :runtime
23
- prerelease: false
24
- version_requirements: !ruby/object:Gem::Requirement
25
- none: false
26
- requirements:
27
- - - ! '>='
28
- - !ruby/object:Gem::Version
29
- version: 0.0.1
30
13
  - !ruby/object:Gem::Dependency
31
14
  name: ffi
32
15
  requirement: !ruby/object:Gem::Requirement
33
- none: false
34
16
  requirements:
35
- - - ! '>='
17
+ - - ">="
36
18
  - !ruby/object:Gem::Version
37
- version: 0.0.1
19
+ version: '0'
38
20
  type: :runtime
39
21
  prerelease: false
40
22
  version_requirements: !ruby/object:Gem::Requirement
41
- none: false
42
- requirements:
43
- - - ! '>='
44
- - !ruby/object:Gem::Version
45
- version: 0.0.1
46
- - !ruby/object:Gem::Dependency
47
- name: rdoc
48
- requirement: !ruby/object:Gem::Requirement
49
- none: false
50
- requirements:
51
- - - ~>
52
- - !ruby/object:Gem::Version
53
- version: '4.0'
54
- type: :development
55
- prerelease: false
56
- version_requirements: !ruby/object:Gem::Requirement
57
- none: false
58
23
  requirements:
59
- - - ~>
24
+ - - ">="
60
25
  - !ruby/object:Gem::Version
61
- version: '4.0'
26
+ version: '0'
62
27
  - !ruby/object:Gem::Dependency
63
- name: newgem
28
+ name: bundler
64
29
  requirement: !ruby/object:Gem::Requirement
65
- none: false
66
30
  requirements:
67
- - - ! '>='
31
+ - - "~>"
68
32
  - !ruby/object:Gem::Version
69
- version: 1.5.3
33
+ version: '1.7'
70
34
  type: :development
71
35
  prerelease: false
72
36
  version_requirements: !ruby/object:Gem::Requirement
73
- none: false
74
37
  requirements:
75
- - - ! '>='
38
+ - - "~>"
76
39
  - !ruby/object:Gem::Version
77
- version: 1.5.3
40
+ version: '1.7'
78
41
  - !ruby/object:Gem::Dependency
79
- name: hoe
42
+ name: rake
80
43
  requirement: !ruby/object:Gem::Requirement
81
- none: false
82
44
  requirements:
83
- - - ~>
45
+ - - "~>"
84
46
  - !ruby/object:Gem::Version
85
- version: '3.6'
47
+ version: '10.0'
86
48
  type: :development
87
49
  prerelease: false
88
50
  version_requirements: !ruby/object:Gem::Requirement
89
- none: false
90
51
  requirements:
91
- - - ~>
52
+ - - "~>"
92
53
  - !ruby/object:Gem::Version
93
- version: '3.6'
94
- description: ! "scbi_fqbin is a gem to handle compressed fastq and fasta files (FQbin
95
- files) made by Rafael Larrosa, Gonzalo Claros & Dario Guerrero for the Plataforma
96
- Andaluza de Bioinformática.\n\nFastaBin was developed to handle huge fasta and qual
97
- files in a more efficient manner. To achieve its goals, FastaBin uses some \nindexing
98
- and compression techniques in order to minimize disk accesses and thus increase
99
- the performance when reading fasta and qual files."
54
+ version: '10.0'
55
+ description: Read/write compressed fastq or fasta files in fqbin format
100
56
  email:
101
- - dariogf@gmail.com
57
+ - dariogf@scbi.uma.es
102
58
  executables: []
103
59
  extensions: []
104
- extra_rdoc_files:
105
- - History.txt
106
- - Manifest.txt
107
- - PostInstall.txt
108
- - README.rdoc
60
+ extra_rdoc_files: []
109
61
  files:
110
- - History.txt
111
- - Manifest.txt
112
- - PostInstall.txt
113
- - README.rdoc
62
+ - ".DS_Store"
63
+ - ".gitignore"
64
+ - Gemfile
65
+ - LICENSE.txt
66
+ - README.md
114
67
  - Rakefile
115
- - script/console
116
- - script/destroy
117
- - script/generate
118
- - lib/scbi_fqbin/fbin_file.rb
119
68
  - lib/scbi_fqbin.rb
69
+ - lib/scbi_fqbin/fastabin.rb
70
+ - lib/scbi_fqbin/fastq_file_c.rb
71
+ - lib/scbi_fqbin/fbin_file.rb
72
+ - lib/scbi_fqbin/t.rb
73
+ - lib/scbi_fqbin/t2.rb
74
+ - lib/scbi_fqbin/version.rb
75
+ - lib_fqbin_src.zip
76
+ - lib_fqbin_src/Makefile
77
+ - lib_fqbin_src/fq
78
+ - lib_fqbin_src/fq.c
79
+ - lib_fqbin_src/hash_fqbin
80
+ - lib_fqbin_src/hash_fqbin.c
81
+ - lib_fqbin_src/idx_fqbin
82
+ - lib_fqbin_src/iterate_fqbin
83
+ - lib_fqbin_src/iterate_fqbin.c
84
+ - lib_fqbin_src/lib_fqbin.c
85
+ - lib_fqbin_src/lib_fqbin.h
86
+ - lib_fqbin_src/mk_fqbin
87
+ - lib_fqbin_src/mk_fqbin.c
88
+ - lib_fqbin_src/other/bwxform.c
89
+ - lib_fqbin_src/other/bwxform.h
90
+ - lib_fqbin_src/other/find_in_index.c
91
+ - lib_fqbin_src/other/hash_fbin_nogzchunks.c
92
+ - lib_fqbin_src/other/idx_fqbin
93
+ - lib_fqbin_src/other/idx_fqbin.c
94
+ - lib_fqbin_src/other/make_hsh.sh
95
+ - lib_fqbin_src/other/rd_extras_fbin.c
96
+ - lib_fqbin_src/read_fq
97
+ - lib_fqbin_src/read_fq.c
98
+ - lib_fqbin_src/read_fqbin
99
+ - lib_fqbin_src/read_fqbin.c
100
+ - lib_fqbin_src/sort_index
101
+ - lib_fqbin_src/test.rb
102
+ - scbi_fqbin.gemspec
103
+ - test/build.rake
104
+ - test/fbinfile
105
+ - test/fbinfile.index
106
+ - test/no_test_fill_file.rb
107
+ - test/old/app.rb
108
+ - test/old/bin/iterate_fastabin.rb
109
+ - test/old/bin/mk_fastabin.rb
110
+ - test/old/bin/rd_fastabin.rb
111
+ - test/old/bin/rd_fq.rb
112
+ - test/old/bioruby.rb
113
+ - test/old/c/Makefile
114
+ - test/old/c/fbin_lib.zip
115
+ - test/old/c/iterate_fbin.c
116
+ - test/old/c/liblibreria_gz.a
117
+ - test/old/c/libreria_gz.c
118
+ - test/old/c/libreria_gz.h
119
+ - test/old/c/main.c
120
+ - test/old/c/mk_fbin.c
121
+ - test/old/c/rd_seq_fbin.c
122
+ - test/old/c/test_ffi/a.out
123
+ - test/old/c/test_ffi/app.c
124
+ - test/old/c/test_ffi/app.o
125
+ - test/old/c/test_ffi/app.rb
126
+ - test/old/c/test_ffi/liblibreria_gz.dylib
127
+ - test/old/c/test_ffi/libmylibrary.dylib
128
+ - test/old/c/test_ffi/my_library.rb
129
+ - test/old/c/test_ffi/mylibrary.c
130
+ - test/old/c/test_ffi/mylibrary.h
131
+ - test/old/c/test_ffi/mylibrary.o
132
+ - test/old/c/usage_instructions.txt
133
+ - test/old/ext/Makefile
134
+ - test/old/ext/Makefile.dario
135
+ - test/old/ext/extconf.rb
136
+ - test/old/ext/mk_fbin.c
137
+ - test/old/ext/mkmf.log
138
+ - test/old/ext/sample/extras.txt
139
+ - test/old/ext/sample/extras2.txt
140
+ - test/old/ext/sample/f1.fasta
141
+ - test/old/ext/sample/f1.fasta.qual
142
+ - test/old/ext/sample/f1.fbin
143
+ - test/old/ext/sample/f1.fbin.index
144
+ - test/old/ext/sample/main.c
145
+ - test/old/ext/usage_instructions.txt
146
+ - test/old/t_scbi_fastabin.rb
147
+ - test/read_tests/10-original_sizes.sh
148
+ - test/read_tests/20-fq_time.sh
149
+ - test/read_tests/30-fbin_read_time.sh
150
+ - test/read_tests/40-bsc_read_time.sh
151
+ - test/read_tests/50-fq_time_x4.sh
152
+ - test/read_tests/60-fbin_read_time_x4.sh
153
+ - test/read_tests/70-bsc_read_time_x4.sh
154
+ - test/results_bio_scbi_fasta.txt
155
+ - test/scbi_fbin_file_test.rb
156
+ - test/speed.txt
157
+ - test/t_scbi_fasta.rb
120
158
  - test/test_helper.rb
121
- - test/test_scbi_fbin_file.rb
122
- - .gemtest
123
- homepage: http://github.com/dariogf/scbi_fqbin
124
- licenses: []
125
- post_install_message: PostInstall.txt
126
- rdoc_options:
127
- - --main
128
- - README.rdoc
159
+ - test/write_tests/10-original_sizes.sh
160
+ - test/write_tests/20-zip_time.sh
161
+ - test/write_tests/30-mk_fbin_time.sh
162
+ - test/write_tests/31-mk_fbin_time_f30.sh
163
+ - test/write_tests/40-gzip_time.sh
164
+ - test/write_tests/41-bsc_time.sh
165
+ - test/write_tests/50-zip_sizes.sh
166
+ - test/write_tests/60-fbin_sizes.sh
167
+ - test/write_tests/61-fbin_sizes_f30.sh
168
+ - test/write_tests/70-gzip_sizes.sh
169
+ - test/write_tests/80-bsc_sizes.sh
170
+ - website/index.html
171
+ - website/index.txt
172
+ - website/javascripts/rounded_corners_lite.inc.js
173
+ - website/stylesheets/screen.css
174
+ - website/template.html.erb
175
+ homepage: ''
176
+ licenses:
177
+ - MIT
178
+ metadata: {}
179
+ post_install_message:
180
+ rdoc_options: []
129
181
  require_paths:
130
182
  - lib
131
183
  required_ruby_version: !ruby/object:Gem::Requirement
132
- none: false
133
184
  requirements:
134
- - - ! '>='
185
+ - - ">="
135
186
  - !ruby/object:Gem::Version
136
187
  version: '0'
137
188
  required_rubygems_version: !ruby/object:Gem::Requirement
138
- none: false
139
189
  requirements:
140
- - - ! '>='
190
+ - - ">="
141
191
  - !ruby/object:Gem::Version
142
192
  version: '0'
143
193
  requirements: []
144
- rubyforge_project: scbi_fqbin
145
- rubygems_version: 1.8.24
194
+ rubyforge_project:
195
+ rubygems_version: 2.4.4
146
196
  signing_key:
147
- specification_version: 3
148
- summary: scbi_fqbin is a gem to handle compressed fastq and fasta files (FQbin files)
149
- made by Rafael Larrosa, Gonzalo Claros & Dario Guerrero for the Plataforma Andaluza
150
- de Bioinformática
197
+ specification_version: 4
198
+ summary: Read/write compressed fastq or fasta files in fqbin format
151
199
  test_files:
200
+ - test/build.rake
201
+ - test/fbinfile
202
+ - test/fbinfile.index
203
+ - test/no_test_fill_file.rb
204
+ - test/old/app.rb
205
+ - test/old/bin/iterate_fastabin.rb
206
+ - test/old/bin/mk_fastabin.rb
207
+ - test/old/bin/rd_fastabin.rb
208
+ - test/old/bin/rd_fq.rb
209
+ - test/old/bioruby.rb
210
+ - test/old/c/Makefile
211
+ - test/old/c/fbin_lib.zip
212
+ - test/old/c/iterate_fbin.c
213
+ - test/old/c/liblibreria_gz.a
214
+ - test/old/c/libreria_gz.c
215
+ - test/old/c/libreria_gz.h
216
+ - test/old/c/main.c
217
+ - test/old/c/mk_fbin.c
218
+ - test/old/c/rd_seq_fbin.c
219
+ - test/old/c/test_ffi/a.out
220
+ - test/old/c/test_ffi/app.c
221
+ - test/old/c/test_ffi/app.o
222
+ - test/old/c/test_ffi/app.rb
223
+ - test/old/c/test_ffi/liblibreria_gz.dylib
224
+ - test/old/c/test_ffi/libmylibrary.dylib
225
+ - test/old/c/test_ffi/my_library.rb
226
+ - test/old/c/test_ffi/mylibrary.c
227
+ - test/old/c/test_ffi/mylibrary.h
228
+ - test/old/c/test_ffi/mylibrary.o
229
+ - test/old/c/usage_instructions.txt
230
+ - test/old/ext/Makefile
231
+ - test/old/ext/Makefile.dario
232
+ - test/old/ext/extconf.rb
233
+ - test/old/ext/mk_fbin.c
234
+ - test/old/ext/mkmf.log
235
+ - test/old/ext/sample/extras.txt
236
+ - test/old/ext/sample/extras2.txt
237
+ - test/old/ext/sample/f1.fasta
238
+ - test/old/ext/sample/f1.fasta.qual
239
+ - test/old/ext/sample/f1.fbin
240
+ - test/old/ext/sample/f1.fbin.index
241
+ - test/old/ext/sample/main.c
242
+ - test/old/ext/usage_instructions.txt
243
+ - test/old/t_scbi_fastabin.rb
244
+ - test/read_tests/10-original_sizes.sh
245
+ - test/read_tests/20-fq_time.sh
246
+ - test/read_tests/30-fbin_read_time.sh
247
+ - test/read_tests/40-bsc_read_time.sh
248
+ - test/read_tests/50-fq_time_x4.sh
249
+ - test/read_tests/60-fbin_read_time_x4.sh
250
+ - test/read_tests/70-bsc_read_time_x4.sh
251
+ - test/results_bio_scbi_fasta.txt
252
+ - test/scbi_fbin_file_test.rb
253
+ - test/speed.txt
254
+ - test/t_scbi_fasta.rb
152
255
  - test/test_helper.rb
153
- - test/test_scbi_fbin_file.rb
256
+ - test/write_tests/10-original_sizes.sh
257
+ - test/write_tests/20-zip_time.sh
258
+ - test/write_tests/30-mk_fbin_time.sh
259
+ - test/write_tests/31-mk_fbin_time_f30.sh
260
+ - test/write_tests/40-gzip_time.sh
261
+ - test/write_tests/41-bsc_time.sh
262
+ - test/write_tests/50-zip_sizes.sh
263
+ - test/write_tests/60-fbin_sizes.sh
264
+ - test/write_tests/61-fbin_sizes_f30.sh
265
+ - test/write_tests/70-gzip_sizes.sh
266
+ - test/write_tests/80-bsc_sizes.sh