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
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  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
data/doc/table_of_contents.html ADDED
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+ <!DOCTYPE html>
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+
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+ <html>
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+ <head>
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+ <meta charset="UTF-8">
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+
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+ <title>Table of Contents - Pileup</title>
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+
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+ <link href="./fonts.css" rel="stylesheet">
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+ <link href="./rdoc.css" rel="stylesheet">
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+
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+ <script type="text/javascript">
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+ var rdoc_rel_prefix = "./";
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+ </script>
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+
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+ <script src="./js/jquery.js"></script>
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+ <script src="./js/navigation.js"></script>
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+ <script src="./js/search_index.js"></script>
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+ <script src="./js/search.js"></script>
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+ <script src="./js/searcher.js"></script>
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+ <script src="./js/darkfish.js"></script>
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+
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+
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+ <body id="top" class="table-of-contents">
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+ <main role="main">
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+ <h1 class="class">Table of Contents - Pileup</h1>
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+
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+ <h2 id="pages">Pages</h2>
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+ <ul>
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+ <li class="file">
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+ <a href="LICENSE_txt.html">LICENSE</a>
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+ </li>
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+
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+ </ul>
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+
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+ <h2 id="classes">Classes and Modules</h2>
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+ <ul>
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+ <li class="module">
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+ <a href="Bio.html">Bio</a>
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+
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+ <ul>
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+ <li><a href="Bio.html#label-Bio%3A%3ADB%3A%3APileup+">Bio::DB::Pileup </a>
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+ <li><a href="Bio.html#label-Vcf+">Vcf </a>
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+ </ul>
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+ </li>
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+ <li class="class">
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+ <a href="Bio/DB/Alignment.html">Bio::DB::Alignment</a>
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+ </li>
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+ <li class="class">
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+ <a href="Bio/DB/Pileup.html">Bio::DB::Pileup</a>
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+ </li>
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+ <li class="module">
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+ <a href="Bio/DB/SAM/Library.html">Bio::DB::SAM::Library</a>
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+ </li>
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+ <li class="module">
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+ <a href="Bio/DB/SAM/Tools.html">Bio::DB::SAM::Tools</a>
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+ </li>
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+ <li class="class">
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+ <a href="Bio/DB/Sam.html">Bio::DB::Sam</a>
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+ </li>
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+ <li class="class">
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+ <a href="Bio/DB/Tag.html">Bio::DB::Tag</a>
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+ </li>
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+ <li class="class">
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+ <a href="Bio/DB/Vcf.html">Bio::DB::Vcf</a>
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+ </li>
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+ </ul>
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+
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+ <h2 id="methods">Methods</h2>
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+ <ul>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Sam.html#method-c-docs">::docs</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/SAM/Library.html#method-c-filename">::filename</a>
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+ &mdash;
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+ <span class="container">Bio::DB::SAM::Library</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Pileup.html#method-c-iupac_to_base">::iupac_to_base</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Pileup</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Pileup.html#method-c-new">::new</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Pileup</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Alignment.html#method-c-new">::new</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Alignment</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Vcf.html#method-c-new">::new</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Vcf</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Sam.html#method-c-new">::new</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+ <li class="method">
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+ <a href="Bio/DB/Sam.html#method-i-average_coverage">#average_coverage</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+ <li class="method">
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+ <a href="Bio/DB/Sam.html#method-i-calmd">#calmd</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+ <li class="method">
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+ <a href="Bio/DB/Sam.html#method-i-cat">#cat</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+ <li class="method">
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+ <a href="Bio/DB/Sam.html#method-i-chromosome_coverage">#chromosome_coverage</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+ <li class="method">
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+ <a href="Bio/DB/Sam.html#method-i-depth">#depth</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+ <li class="method">
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+ <a href="Bio/DB/Sam.html#method-i-faidx">#faidx</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+ <li class="method">
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+ <a href="Bio/DB/Sam.html#method-i-fetch">#fetch</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+ <a href="Bio/DB/Sam.html#method-i-fetch_reference">#fetch_reference</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+ <a href="Bio/DB/Sam.html#method-i-fetch_with_function">#fetch_with_function</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+ <a href="Bio/DB/Sam.html#method-i-fix_mates">#fix_mates</a>
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+ <span class="container">Bio::DB::Sam</span>
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+ <a href="Bio/DB/Sam.html#method-i-fixmate">#fixmate</a>
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+ <span class="container">Bio::DB::Sam</span>
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+ <a href="Bio/DB/Sam.html#method-i-flag_stats">#flag_stats</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+ <a href="Bio/DB/Sam.html#method-i-flagstat">#flagstat</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+ <li class="method">
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+ <a href="Bio/DB/Pileup.html#method-i-genotype_list">#genotype_list</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Pileup</span>
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+ <li class="method">
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+ <a href="Bio/DB/Sam.html#method-i-idxstats">#idxstats</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+ <li class="method">
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+ <a href="Bio/DB/Sam.html#method-i-index">#index</a>
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+ <span class="container">Bio::DB::Sam</span>
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+ <li class="method">
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+ <a href="Bio/DB/Sam.html#method-i-index_stats">#index_stats</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+ <li class="method">
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+ <a href="Bio/DB/Vcf.html#method-i-int_or_raw">#int_or_raw</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Vcf</span>
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+ <li class="method">
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+ <a href="Bio/DB/Sam.html#method-i-merge">#merge</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+ <li class="method">
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+ <a href="Bio/DB/Sam.html#method-i-mpileup">#mpileup</a>
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+ <span class="container">Bio::DB::Sam</span>
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+ <a href="Bio/DB/Pileup.html#method-i-non_ref_count">#non_ref_count</a>
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+ <span class="container">Bio::DB::Pileup</span>
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+ <li class="method">
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+ <a href="Bio/DB/Pileup.html#method-i-non_refs">#non_refs</a>
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+ <span class="container">Bio::DB::Pileup</span>
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+ <li class="method">
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+ <a href="Bio/DB/Sam.html#method-i-open">#open</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+ <li class="method">
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+ <a href="Bio/DB/Pileup.html#method-i-parse_indel">#parse_indel</a>
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+ <span class="container">Bio::DB::Pileup</span>
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+ <li class="method">
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+ <a href="Bio/DB/Vcf.html#method-i-parse_line">#parse_line</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Vcf</span>
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+ <li class="method">
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+ <a href="Bio/DB/Sam.html#method-i-phase">#phase</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Sam.html#method-i-plot_chromosome_coverage">#plot_chromosome_coverage</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Pileup.html#method-i-ref_count">#ref_count</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Pileup</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Sam.html#method-i-reheader">#reheader</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Sam.html#method-i-remove_duplicates">#remove_duplicates</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+ <li class="method">
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+ <a href="Bio/DB/Sam.html#method-i-rmdup">#rmdup</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Tag.html#method-i-set">#set</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Tag</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Sam.html#method-i-sort">#sort</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+ <li class="method">
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+ <a href="Bio/DB/Sam.html#method-i-targetcut">#targetcut</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+ <li class="method">
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+ <a href="Bio/DB/Pileup.html#method-i-to_s">#to_s</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Pileup</span>
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+ <li class="method">
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+ <a href="Bio/DB/Pileup.html#method-i-to_vcf">#to_vcf</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Pileup</span>
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+ <li class="method">
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+ <a href="Bio/DB/Sam.html#method-i-tview">#tview</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+ <li class="method">
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+ <a href="Bio/DB/Sam.html#method-i-view">#view</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+ </ul>
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+ </main>
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+
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+ <footer id="validator-badges" role="contentinfo">
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+ <p><a href="http://validator.w3.org/check/referer">Validate</a>
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+ <p>Generated by <a href="http://rdoc.rubyforge.org">RDoc</a> 4.1.1.
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+ <p>Based on <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish</a> by <a href="http://deveiate.org">Michael Granger</a>.
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+ </footer>
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+
data/ext/Makefile-bioruby.patch ADDED
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+ --- Makefile.bk 2014-02-01 19:56:14.000000000 +0000
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+ +++ Makefile 2014-02-01 20:47:30.000000000 +0000
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+ @@ -1,7 +1,7 @@
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+ CC= gcc
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+ -CFLAGS= -g -Wall -O2
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+ +CFLAGS= -g -Wall -O2 -fPIC
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+ #LDFLAGS= -Wl,-rpath,\$$ORIGIN/../lib
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+ -DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1
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+ +DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0
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+ KNETFILE_O= knetfile.o
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+ LOBJS= bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o \
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+ bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o \
data/ext/Makefile-suse.patch ADDED
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+ --- Makefile 2013-12-10 14:06:29.868639418 +0000
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+ +++ Makefile.opensuse 2013-12-10 14:06:56.548222174 +0000
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+ @@ -13,7 +13,7 @@
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+ INCLUDES= -I.
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+ SUBDIRS= . bcftools misc
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+ LIBPATH=
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+ -LIBCURSES= -lcurses # -lXCurses
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+ +LIBCURSES= -lncurses # -lXCurses
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+
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+ .SUFFIXES:.c .o
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+
data/ext/mkrf_conf.rb ADDED
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+ #(c) Copyright 2011 Raoul Bonnal. All Rights Reserved.
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+
3
+ # create Rakefile for shared library compilation
4
+
5
+
6
+
7
+ path = File.expand_path(File.dirname(__FILE__))
8
+
9
+ path_external = File.join(path, "../lib/bio/db/sam/external")
10
+
11
+ require 'rbconfig'
12
+
13
+ if is_windows = (RbConfig::CONFIG['host_os'] =~ /mswin|mingw|cygwin/)
14
+ SamToolsFile = "samtools.zip"
15
+
16
+ File.open(File.join(path,"Rakefile"),"w") do |rakefile|
17
+ rakefile.write <<-RAKE
18
+ require 'rbconfig'
19
+ require 'open-uri'
20
+ require 'fileutils'
21
+ include FileUtils::Verbose
22
+ require 'rake/clean'
23
+
24
+ url = "http://download-codeplex.sec.s-msft.com/Download/Release?ProjectName=bow&DownloadId=379402&FileTime=129956483945970000&Build=21040"
25
+
26
+ task :download do
27
+ #TODO dont run if —local
28
+ open(url) do |uri|
29
+ File.open("#{SamToolsFile}",'wb') do |fout|
30
+ fout.write(uri.read)
31
+ end #fout
32
+ end #uri
33
+ end
34
+
35
+ task :save do
36
+ sh "unzip #{SamToolsFile} -d samtools-windows"
37
+ cd("samtools-windows") do
38
+ cp('samtools.exe', "#{path_external}")
39
+ end #cd
40
+ end
41
+
42
+ task :clean do
43
+ rm_rf("samtools-windows")
44
+ rm_rf("#{SamToolsFile}")
45
+ end
46
+
47
+ task :default => [:download, :save, :clean]
48
+
49
+ RAKE
50
+
51
+ end
52
+ else
53
+ version = File.open(File.join(path_external,"VERSION"),'r')
54
+ Version = version.read
55
+ version.close
56
+ #TODO if local instalarion, make sure that the paths of the gzip files exist. the version shoulf match the supported version of samtools in the library
57
+ #url = "http://sourceforge.net/projects/samtools/files/samtools/#{Version}/samtools-#{Version}.tar.bz2/download"
58
+ url="http://github.com/samtools/samtools/releases/download/#{Version}/samtools-#{Version}.tar.bz2"
59
+ SamToolsFile = "samtools-#{Version}.tar.bz2"
60
+ url_bcftools="http://github.com/samtools/bcftools/releases/download/#{Version}/bcftools-#{Version}.tar.bz2"
61
+ BcfToolsFile = "bcftools-#{Version}.tar.bz2"
62
+
63
+ File.open(File.join(path,"Rakefile"),"w") do |rakefile|
64
+ rakefile.write <<-RAKE
65
+ require 'rbconfig'
66
+ require 'open-uri'
67
+ #require 'open_uri_redirections'
68
+ require 'fileutils'
69
+ include FileUtils::Verbose
70
+ require 'rake/clean'
71
+
72
+ URL = "#{url}"
73
+ URL_bcf = "#{url_bcftools}"
74
+ task :download do
75
+ URI.open(URL) do |uri|
76
+ File.open("#{SamToolsFile}",'wb') do |fout|
77
+ fout.write(uri.read)
78
+ end #fout
79
+ end #uri
80
+
81
+ URI.open(URL_bcf) do |uri|
82
+ File.open("#{BcfToolsFile}",'wb') do |fout|
83
+ fout.write(uri.read)
84
+ end #fout
85
+ end #uri
86
+
87
+ end
88
+
89
+ task :compile do
90
+ sh "tar xvfj #{SamToolsFile}"
91
+ cd("samtools-#{Version}") do
92
+ sh "make"
93
+ cp('samtools', "#{path_external}")
94
+ end #cd
95
+
96
+ sh "tar xvfj #{BcfToolsFile}"
97
+ cd("bcftools-#{Version}") do
98
+ sh "make"
99
+ cp('bcftools', "#{path_external}")
100
+ end #cd
101
+ end
102
+
103
+ task :clean do
104
+ cd("samtools-#{Version}") do
105
+ sh "make clean"
106
+ end
107
+ rm("#{SamToolsFile}")
108
+ rm_rf("samtools-#{Version}")
109
+ rm("#{BcfToolsFile}")
110
+ rm_rf("bcftools-#{Version}")
111
+ end
112
+
113
+ task :default => [:download, :compile, :clean]
114
+
115
+ RAKE
116
+
117
+ end
118
+ end
data/lib/bio/BIOExtensions.rb ADDED
@@ -0,0 +1,89 @@
1
+ class Bio::NucleicAcid
2
+
3
+ IUPAC_CODES = {
4
+
5
+ 'y' => 'ct',
6
+ 'r' => 'ag',
7
+ 'w' => 'at',
8
+ 's' => 'cg',
9
+ 'k' => 'gt',
10
+ 'm' => 'ac',
11
+
12
+ 'b' => 'cgt',
13
+ 'd' => 'agt',
14
+ 'h' => 'act',
15
+ 'v' => 'acg',
16
+
17
+ 'n' => 'acgt',
18
+
19
+ 'a' => 'a',
20
+ 't' => 't',
21
+ 'g' => 'g',
22
+ 'c' => 'c',
23
+ 'u' => 'u',
24
+
25
+ 'ct' => 'y',
26
+ 'ag' => 'r',
27
+ 'at' => 'w',
28
+ 'cg' => 's',
29
+ 'gt' => 'k',
30
+ 'ac' => 'm',
31
+
32
+ 'cgt' => 'b',
33
+ 'agt' => 'd',
34
+ 'act' => 'h',
35
+ 'acg' => 'v',
36
+
37
+ 'acgt' => 'n'
38
+ }
39
+
40
+
41
+ def self.is_unambiguous(base)
42
+ "acgtACGT".match(base)
43
+ end
44
+
45
+ def self.to_IUAPC(bases)
46
+ base = IUPAC_CODES[bases.to_s.downcase.chars.sort.uniq.join]
47
+ if base == nil
48
+ p "Invalid base! #{base}"
49
+ base = 'n' #This is a patch... as one of the scripts failed here.
50
+ end
51
+ base.upcase
52
+ end
53
+
54
+ def self.is_valid(code, base)
55
+ IUPAC_CODES[code.downcase].chars.include? base.downcase
56
+ end
57
+
58
+ end
59
+
60
+ #Monkey patching to Bio::Sequence to find snps between sequences. It assumes the
61
+ #sequences are already aligned and doesn't check if a base on the first sequence is
62
+ #valid on the second.
63
+ class Bio::Sequence
64
+ def self.snps_between(seq1, seq2)
65
+ snps=0
66
+ for i in (0..seq1.size-1)
67
+ snps += 1 if seq1[i] != seq2[i]
68
+ end
69
+ snps
70
+ end
71
+ end
72
+
73
+ class String
74
+ #Monkey patching to count how many ambiguity codes are present in the string, for Nucleic Acids
75
+ def count_ambiguities
76
+ snps=0
77
+
78
+ for i in (0..self.size-1)
79
+
80
+ snps += 1 if !Bio::NucleicAcid.is_unambiguous(self[i])
81
+ end
82
+ snps
83
+ end
84
+
85
+ #Counts how many bases are uppercase
86
+ def upper_case_count
87
+ match(/[^A-Z]*/).to_s.size
88
+ end
89
+ end
data/lib/bio/db/alignment.rb ADDED
@@ -0,0 +1,64 @@
1
+ module Bio
2
+ class DB
3
+
4
+ #a class to represent the SAM OPT values, presented in SAM as TAG:VTYPE:VALUE
5
+ class Tag
6
+ attr_accessor :tag, :type, :value
7
+ def set(str)
8
+ @tag = str[0..1]
9
+ @type = str[3]
10
+ @value = str[5..-1]
11
+ end
12
+ end
13
+
14
+ #Attrobites for the flag field (see chapter 2.2.2 of the sam file documentation)
15
+ #query_strand and mate_strand are true if they are forward. It is the opposite to
16
+ #the definition in the BAM format for clarity.
17
+ #primary is the negation of is_negative from the BAM format
18
+ class Alignment
19
+ attr_accessor :qname, :flag, :rname,:pos,:mapq,:cigar, :mrnm, :mpos, :isize, :seq, :qual, :tags, :al, :samstr, :calend, :qlen
20
+
21
+ attr_accessor :sam_string, :is_paired, :is_mapped, :query_unmapped, :mate_unmapped, :query_strand, :mate_strand, :first_in_pair,:second_in_pair, :primary, :failed_quality, :is_duplicate
22
+
23
+ #parses the SAM string into its constituents and set its attributes
24
+ def initialize(sam_string)
25
+ s = sam_string.chomp.split("\t")
26
+ @sam_string = sam_string
27
+ @qname = s[0]
28
+ @flag = s[1].to_i
29
+ @rname = s[2]
30
+ @pos = s[3].to_i
31
+ @mapq = s[4].to_i
32
+ @cigar = s[5]
33
+ @mrnm = s[6]
34
+ @mpos = s[7].to_i
35
+ @isize = s[8].to_i
36
+ @seq = s[9]
37
+ @qual = s[10]
38
+ @tags = {}
39
+ 11.upto(s.size-1) {|n|
40
+ t = Bio::DB::Tag.new
41
+ t.set(s[n])
42
+ tags[t.tag] = t
43
+ }
44
+
45
+ @is_paired = (@flag & 0x0001) > 0
46
+ @is_mapped = @flag & 0x0002 > 0
47
+ @query_unmapped = @flag & 0x0004 > 0
48
+ @mate_unmapped = @flag & 0x0008 > 0
49
+ @query_strand = !(@flag & 0x0010 > 0)
50
+ @mate_strand = !(@flag & 0x0020 > 0)
51
+ @first_in_pair = @flag & 0x0040 > 0
52
+ @second_in_pair = @flag & 0x0080 > 0
53
+ @primary = !(@flag & 0x0100 > 0)
54
+ @failed_quality = @flag & 0x0200 > 0
55
+ @is_duplicate = @flag & 0x0400 > 0
56
+
57
+ end
58
+
59
+ def to_fastq
60
+ ["@#{qname}",seq, "+",qual].join "\n"
61
+ end
62
+ end
63
+ end
64
+ end