bio-samtools-wrapper 2.7.0

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Files changed (125) hide show
  1. checksums.yaml +7 -0
  2. data/.document +5 -0
  3. data/.travis.yml +27 -0
  4. data/Gemfile +20 -0
  5. data/LICENSE.txt +702 -0
  6. data/README.md +501 -0
  7. data/Rakefile +73 -0
  8. data/VERSION +1 -0
  9. data/bin/bam_consensus.rb +85 -0
  10. data/bio-samtools-wrapper.gemspec +181 -0
  11. data/doc/Bio/DB/Alignment.html +552 -0
  12. data/doc/Bio/DB/Pileup.html +711 -0
  13. data/doc/Bio/DB/SAM/Library.html +167 -0
  14. data/doc/Bio/DB/SAM/Tools.html +109 -0
  15. data/doc/Bio/DB/SAM.html +1853 -0
  16. data/doc/Bio/DB/Tag.html +208 -0
  17. data/doc/Bio/DB/Vcf.html +431 -0
  18. data/doc/Bio/DB.html +105 -0
  19. data/doc/Bio.html +175 -0
  20. data/doc/LICENSE_txt.html +846 -0
  21. data/doc/created.rid +9 -0
  22. data/doc/fonts/Lato-Light.ttf +0 -0
  23. data/doc/fonts/Lato-LightItalic.ttf +0 -0
  24. data/doc/fonts/Lato-Regular.ttf +0 -0
  25. data/doc/fonts/Lato-RegularItalic.ttf +0 -0
  26. data/doc/fonts/SourceCodePro-Bold.ttf +0 -0
  27. data/doc/fonts/SourceCodePro-Regular.ttf +0 -0
  28. data/doc/fonts.css +167 -0
  29. data/doc/images/add.png +0 -0
  30. data/doc/images/arrow_up.png +0 -0
  31. data/doc/images/brick.png +0 -0
  32. data/doc/images/brick_link.png +0 -0
  33. data/doc/images/bug.png +0 -0
  34. data/doc/images/bullet_black.png +0 -0
  35. data/doc/images/bullet_toggle_minus.png +0 -0
  36. data/doc/images/bullet_toggle_plus.png +0 -0
  37. data/doc/images/date.png +0 -0
  38. data/doc/images/delete.png +0 -0
  39. data/doc/images/find.png +0 -0
  40. data/doc/images/loadingAnimation.gif +0 -0
  41. data/doc/images/macFFBgHack.png +0 -0
  42. data/doc/images/package.png +0 -0
  43. data/doc/images/page_green.png +0 -0
  44. data/doc/images/page_white_text.png +0 -0
  45. data/doc/images/page_white_width.png +0 -0
  46. data/doc/images/plugin.png +0 -0
  47. data/doc/images/ruby.png +0 -0
  48. data/doc/images/tag_blue.png +0 -0
  49. data/doc/images/tag_green.png +0 -0
  50. data/doc/images/transparent.png +0 -0
  51. data/doc/images/wrench.png +0 -0
  52. data/doc/images/wrench_orange.png +0 -0
  53. data/doc/images/zoom.png +0 -0
  54. data/doc/index.html +106 -0
  55. data/doc/js/darkfish.js +140 -0
  56. data/doc/js/jquery.js +18 -0
  57. data/doc/js/navigation.js +142 -0
  58. data/doc/js/search.js +109 -0
  59. data/doc/js/search_index.js +1 -0
  60. data/doc/js/searcher.js +228 -0
  61. data/doc/rdoc.css +580 -0
  62. data/doc/table_of_contents.html +305 -0
  63. data/ext/Makefile-bioruby.patch +12 -0
  64. data/ext/Makefile-suse.patch +11 -0
  65. data/ext/mkrf_conf.rb +118 -0
  66. data/lib/bio/BIOExtensions.rb +89 -0
  67. data/lib/bio/db/alignment.rb +64 -0
  68. data/lib/bio/db/fastadb.rb +320 -0
  69. data/lib/bio/db/pileup.rb +273 -0
  70. data/lib/bio/db/sam/external/COPYING +21 -0
  71. data/lib/bio/db/sam/external/VERSION +1 -0
  72. data/lib/bio/db/sam/library.rb +32 -0
  73. data/lib/bio/db/sam.rb +778 -0
  74. data/lib/bio/db/vcf.rb +105 -0
  75. data/lib/bio-samtools-wrapper.rb +9 -0
  76. data/test/.gitignore +1 -0
  77. data/test/helper.rb +18 -0
  78. data/test/sample.vcf +24 -0
  79. data/test/samples/.gitignore +1 -0
  80. data/test/samples/LCI/NC_001988.ffn +2 -0
  81. data/test/samples/LCI/test.bam +0 -0
  82. data/test/samples/LCI/test.bam.bai +0 -0
  83. data/test/samples/small/dupes.bam +0 -0
  84. data/test/samples/small/dupes.sam +274 -0
  85. data/test/samples/small/ids2.txt +1 -0
  86. data/test/samples/small/map_for_reheader.sam +8 -0
  87. data/test/samples/small/map_to_merge1.bam +0 -0
  88. data/test/samples/small/map_to_merge1.bam.bai +0 -0
  89. data/test/samples/small/map_to_merge1.sam +8 -0
  90. data/test/samples/small/map_to_merge2.bam +0 -0
  91. data/test/samples/small/map_to_merge2.bam.bai +0 -0
  92. data/test/samples/small/map_to_merge2.sam +8 -0
  93. data/test/samples/small/no_md.sam +8 -0
  94. data/test/samples/small/sorted.bam +0 -0
  95. data/test/samples/small/sorted.bam.bai +0 -0
  96. data/test/samples/small/test.sai +0 -0
  97. data/test/samples/small/test.tam +10 -0
  98. data/test/samples/small/test_chr.fasta +1000 -0
  99. data/test/samples/small/test_chr.fasta.1.bt2 +0 -0
  100. data/test/samples/small/test_chr.fasta.2.bt2 +0 -0
  101. data/test/samples/small/test_chr.fasta.3.bt2 +0 -0
  102. data/test/samples/small/test_chr.fasta.4.bt2 +0 -0
  103. data/test/samples/small/test_chr.fasta.amb +2 -0
  104. data/test/samples/small/test_chr.fasta.ann +3 -0
  105. data/test/samples/small/test_chr.fasta.bwt +0 -0
  106. data/test/samples/small/test_chr.fasta.pac +0 -0
  107. data/test/samples/small/test_chr.fasta.rbwt +0 -0
  108. data/test/samples/small/test_chr.fasta.rev.1.bt2 +0 -0
  109. data/test/samples/small/test_chr.fasta.rev.2.bt2 +0 -0
  110. data/test/samples/small/test_chr.fasta.rpac +0 -0
  111. data/test/samples/small/test_chr.fasta.rsa +0 -0
  112. data/test/samples/small/test_chr.fasta.sa +0 -0
  113. data/test/samples/small/test_cov.svg +273 -0
  114. data/test/samples/small/test_fastadb.fasta +34 -0
  115. data/test/samples/small/testu.bam +0 -0
  116. data/test/samples/small/testu.bed +2 -0
  117. data/test/test_bio-samtools-wrapper.rb +1 -0
  118. data/test/test_fastadb.rb +89 -0
  119. data/test/test_pileup.rb +90 -0
  120. data/test/test_sam.rb +421 -0
  121. data/test/test_vcf.rb +79 -0
  122. data/tutorial/tutorial.html +474 -0
  123. data/tutorial/tutorial.md +424 -0
  124. data/tutorial/tutorial.pdf +0 -0
  125. metadata +254 -0
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data/.document ADDED
@@ -0,0 +1,5 @@
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+ lib/**/*.rb
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+ bin/*
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+ -
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+ features/**/*.feature
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+ LICENSE.txt
data/.travis.yml ADDED
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+ language: ruby
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+ sudo: false
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+ addons:
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+ apt:
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+ packages:
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+ - zlib1g-dev
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+ - libncurses5-dev
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+ - libtinfo-dev
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+ before_install:
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+ - gem update --system
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+ - if [ $TRAVIS_OS_NAME = osx ]; then brew update; brew install xz ; fi
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+ before_script:
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+ - cd ext
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+ - ruby mkrf_conf.rb
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+ - rake -f Rakefile
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+ - cd ../
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+ os:
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+ - linux
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+ - osx
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+ rvm:
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+ - 2.1.10
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+ - 2.2.5
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+ - 2.3.5
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+ - 2.4.2
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+ - 2.5.0
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+
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+
data/Gemfile ADDED
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+ source "http://rubygems.org"
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+ # Add dependencies required to use your gem here.
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+ # Example:
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+ gem "bio-svgenes", ">= 0.4.1"
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+ gem "bio", ">= 1.4.2"
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+ #gem "rake"
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+ #gem 'open_uri_redirections'
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+
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+ # Add dependencies to develop your gem here.
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+ # Include everything needed to run rake, tests, features, etc.
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+ group :development do
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+ gem "shoulda", "= 2.10"
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+ gem 'test-unit'
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+ if RUBY_VERSION.start_with?("2.1") or RUBY_VERSION.start_with?("2.2") or RUBY_VERSION.start_with?("2.0")
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+ gem "jeweler", "= 2.0.1"
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+ else
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+ gem "juwelier" #, :platforms => :ruby_23 #jeweler support is being dropped
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+ end
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+ gem "rack", "1.6.4", :platforms => :ruby_21
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+ end