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
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  28. data/doc/fonts.css +167 -0
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  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
data/doc/Bio/DB/Alignment.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>class Bio::DB::Alignment - 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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+ <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" role="document" class="class">
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+ <nav role="navigation">
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+ <div id="project-navigation">
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+ <div id="home-section" role="region" title="Quick navigation" class="nav-section">
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+ <h2>
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+ <a href="../../index.html" rel="home">Home</a>
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+ </h2>
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+ <div id="table-of-contents-navigation">
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+ <a href="../../table_of_contents.html#pages">Pages</a>
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+ <a href="../../table_of_contents.html#classes">Classes</a>
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+ <a href="../../table_of_contents.html#methods">Methods</a>
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+ </div>
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+ </div>
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+
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+ <div id="search-section" role="search" class="project-section initially-hidden">
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+ <form action="#" method="get" accept-charset="utf-8">
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+ <div id="search-field-wrapper">
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+ <input id="search-field" role="combobox" aria-label="Search"
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+ aria-autocomplete="list" aria-controls="search-results"
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+ type="text" name="search" placeholder="Search" spellcheck="false"
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+ title="Type to search, Up and Down to navigate, Enter to load">
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+ </div>
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+
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+ <ul id="search-results" aria-label="Search Results"
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+ aria-busy="false" aria-expanded="false"
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+ aria-atomic="false" class="initially-hidden"></ul>
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+ </form>
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+ </div>
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+ </div>
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+
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+
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+
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+ <div id="class-metadata">
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+
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+ <div id="parent-class-section" class="nav-section">
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+ <h3>Parent</h3>
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+
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+
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+ <p class="link">Object
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+
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+ </div>
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+
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+
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+
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+ <!-- Method Quickref -->
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+ <div id="method-list-section" class="nav-section">
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+ <h3>Methods</h3>
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+
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+ <ul class="link-list" role="directory">
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+
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+ <li ><a href="#method-c-new">::new</a>
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+ </ul>
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+ </div>
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+ </div>
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+ </nav>
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+
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+ <main role="main" aria-labelledby="class-Bio::DB::Alignment">
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+ <h1 id="class-Bio::DB::Alignment" class="class">
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+ class Bio::DB::Alignment
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+ </h1>
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+
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+ <section class="description">
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+
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+ <p>Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
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+ documentation) <a
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+ href="Alignment.html#attribute-i-query_strand">#query_strand</a> and <a
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+ href="Alignment.html#attribute-i-mate_strand">#mate_strand</a> are true if
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+ they are forward. It is the opposite to the definition in the BAM format
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+ for clarity. primary is the negation of is_negative from the BAM format</p>
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+
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+ </section>
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+ <section id="5Buntitled-5D" class="documentation-section">
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+ <section class="attribute-method-details" class="method-section">
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+ <header>
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+ <h3>Attributes</h3>
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+ </header>
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+
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+
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+ <div id="attribute-i-al" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">al</span><span
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+ class="attribute-access-type">[RW]</span>
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+ </div>
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+ <div id="attribute-i-calend" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">calend</span><span
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+ class="attribute-access-type">[RW]</span>
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+ </div>
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+ <div id="attribute-i-cigar" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">cigar</span><span
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+ class="attribute-access-type">[RW]</span>
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+ </div>
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+ <div class="method-description">
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+ </div>
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+ </div>
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+ <div id="attribute-i-failed_quality" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">failed_quality</span><span
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+ class="attribute-access-type">[RW]</span>
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+ <div id="attribute-i-first_in_pair" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">first_in_pair</span><span
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+ class="attribute-access-type">[RW]</span>
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+ </div>
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">flag</span><span
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+ <div id="attribute-i-is_duplicate" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">is_duplicate</span><span
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+ class="attribute-access-type">[RW]</span>
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+ </div>
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+ <div id="attribute-i-is_mapped" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">is_mapped</span><span
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+ class="attribute-access-type">[RW]</span>
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+ </div>
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+ <div id="attribute-i-is_paired" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">is_paired</span><span
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+ class="attribute-access-type">[RW]</span>
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+ <span class="method-name">isize</span><span
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+ class="attribute-access-type">[RW]</span>
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+ <div class="method-description">
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+ </div>
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+ <div id="attribute-i-mapq" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">mapq</span><span
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+ class="attribute-access-type">[RW]</span>
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+ </div>
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+ <div class="method-description">
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+ </div>
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+ </div>
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+ <div id="attribute-i-mate_strand" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">mate_strand</span><span
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+ class="attribute-access-type">[RW]</span>
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+ </div>
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+ <div class="method-description">
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+ </div>
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+ <div id="attribute-i-mate_unmapped" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">mate_unmapped</span><span
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+ <span class="method-name">mpos</span><span
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+ class="attribute-access-type">[RW]</span>
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+ <span class="method-name">mrnm</span><span
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+ class="attribute-access-type">[RW]</span>
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+ <span class="method-name">pos</span><span
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+ class="attribute-access-type">[RW]</span>
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+ <span class="method-name">primary</span><span
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+ class="attribute-access-type">[RW]</span>
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+ <div id="attribute-i-qlen" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">qlen</span><span
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+ class="attribute-access-type">[RW]</span>
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+ </div>
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+ </div>
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+ </div>
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+ <div id="attribute-i-qname" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">qname</span><span
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+ class="attribute-access-type">[RW]</span>
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+ <span class="method-name">qual</span><span
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+ <span class="method-name">query_strand</span><span
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+ <span class="method-name">query_unmapped</span><span
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+ <span class="method-name">rname</span><span
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+ <span class="method-name">samstr</span><span
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">second_in_pair</span><span
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+ class="attribute-access-type">[RW]</span>
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+ </div>
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+ <div id="attribute-i-seq" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">seq</span><span
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+ </div>
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+ </div>
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+ </div>
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+
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+ <div id="attribute-i-tags" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">tags</span><span
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+ class="attribute-access-type">[RW]</span>
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+ </div>
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+
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+ <div class="method-description">
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+
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+
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+
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+ </div>
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+ </div>
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+
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+ </section>
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+
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+
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+
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+ <section id="public-class-5Buntitled-5D-method-details" class="method-section">
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+ <header>
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+ <h3>Public Class Methods</h3>
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+ </header>
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+
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+
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+ <div id="method-c-new" class="method-detail ">
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+
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+ <div class="method-heading">
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+ <span class="method-name">new</span><span
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+ class="method-args">(sam_string)</span>
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+
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+ <span class="method-click-advice">click to toggle source</span>
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+
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+ </div>
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+
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+
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+ <div class="method-description">
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+
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+ <p>parses the SAM string into its constituents and set its attributes</p>
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+
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+
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+
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+
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+ <div class="method-source-code" id="new-source">
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+ <pre><span class="ruby-comment"># File lib/bio/db/alignment.rb, line 24</span>
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+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">sam_string</span>)
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+ <span class="ruby-identifier">s</span> = <span class="ruby-identifier">sam_string</span>.<span class="ruby-identifier">chomp</span>.<span class="ruby-identifier">split</span>(<span class="ruby-string">&quot;\t&quot;</span>)
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+ <span class="ruby-ivar">@qname</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">0</span>]
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+ <span class="ruby-ivar">@flag</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">1</span>].<span class="ruby-identifier">to_i</span>
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+ <span class="ruby-ivar">@rname</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">2</span>]
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+ <span class="ruby-ivar">@pos</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">3</span>].<span class="ruby-identifier">to_i</span>
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+ <span class="ruby-ivar">@mapq</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">4</span>].<span class="ruby-identifier">to_i</span>
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+ <span class="ruby-ivar">@cigar</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">5</span>]
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+ <span class="ruby-ivar">@mrnm</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">6</span>]
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+ <span class="ruby-ivar">@mpos</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">7</span>].<span class="ruby-identifier">to_i</span>
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+ <span class="ruby-ivar">@isize</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">8</span>].<span class="ruby-identifier">to_i</span>
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+ <span class="ruby-ivar">@seq</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">9</span>]
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+ <span class="ruby-ivar">@qual</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">10</span>]
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+ <span class="ruby-ivar">@tags</span> = {}
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+ <span class="ruby-value">11</span>.<span class="ruby-identifier">upto</span>(<span class="ruby-identifier">s</span>.<span class="ruby-identifier">size</span><span class="ruby-operator">-</span><span class="ruby-value">1</span>) {<span class="ruby-operator">|</span><span class="ruby-identifier">n</span><span class="ruby-operator">|</span>
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+ <span class="ruby-identifier">t</span> = <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">DB</span><span class="ruby-operator">::</span><span class="ruby-constant">Tag</span>.<span class="ruby-identifier">new</span>
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+ <span class="ruby-identifier">t</span>.<span class="ruby-identifier">set</span>(<span class="ruby-identifier">s</span>[<span class="ruby-identifier">n</span>])
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+ <span class="ruby-identifier">tags</span>[<span class="ruby-identifier">t</span>.<span class="ruby-identifier">tag</span>] = <span class="ruby-identifier">t</span>
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+ }
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+
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+ <span class="ruby-ivar">@is_paired</span> = (<span class="ruby-ivar">@flag</span> <span class="ruby-operator">&amp;</span> <span class="ruby-value">0x0001</span>) <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>
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+ <span class="ruby-ivar">@is_mapped</span> = <span class="ruby-ivar">@flag</span> <span class="ruby-operator">&amp;</span> <span class="ruby-value">0x0002</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>
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+ <span class="ruby-ivar">@query_unmapped</span> = <span class="ruby-ivar">@flag</span> <span class="ruby-operator">&amp;</span> <span class="ruby-value">0x0004</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>
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+ <span class="ruby-ivar">@mate_unmapped</span> = <span class="ruby-ivar">@flag</span> <span class="ruby-operator">&amp;</span> <span class="ruby-value">0x0008</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>
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+ <span class="ruby-ivar">@query_strand</span> = <span class="ruby-operator">!</span>(<span class="ruby-ivar">@flag</span> <span class="ruby-operator">&amp;</span> <span class="ruby-value">0x0010</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>)
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+ <span class="ruby-ivar">@mate_strand</span> = <span class="ruby-operator">!</span>(<span class="ruby-ivar">@flag</span> <span class="ruby-operator">&amp;</span> <span class="ruby-value">0x0020</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>)
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+ <span class="ruby-ivar">@first_in_pair</span> = <span class="ruby-ivar">@flag</span> <span class="ruby-operator">&amp;</span> <span class="ruby-value">0x0040</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>
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+ <span class="ruby-ivar">@second_in_pair</span> = <span class="ruby-ivar">@flag</span> <span class="ruby-operator">&amp;</span> <span class="ruby-value">0x0080</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>
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+ <span class="ruby-ivar">@primary</span> = <span class="ruby-operator">!</span>(<span class="ruby-ivar">@flag</span> <span class="ruby-operator">&amp;</span> <span class="ruby-value">0x0100</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>)
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+ <span class="ruby-ivar">@failed_quality</span> = <span class="ruby-ivar">@flag</span> <span class="ruby-operator">&amp;</span> <span class="ruby-value">0x0200</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>
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+ <span class="ruby-ivar">@is_duplicate</span> = <span class="ruby-ivar">@flag</span> <span class="ruby-operator">&amp;</span> <span class="ruby-value">0x0400</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>
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+
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+ <span class="ruby-keyword">end</span></pre>
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+ </div>
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+
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+ </div>
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+
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+
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+
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+
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+ </div>
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+
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+
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+ </section>
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+
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+ </section>
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+ </main>
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+
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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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+