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/Bio/DB/Pileup.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::Pileup - 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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+ <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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+
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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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+ <div id="class-metadata">
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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-iupac_to_base">::iupac_to_base</a>
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+
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+ <li ><a href="#method-c-new">::new</a>
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+
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+ <li ><a href="#method-i-genotype_list">#genotype_list</a>
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+
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+ <li ><a href="#method-i-non_ref_count">#non_ref_count</a>
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+
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+ <li ><a href="#method-i-non_refs">#non_refs</a>
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+
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+ <li ><a href="#method-i-parse_indel">#parse_indel</a>
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+
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+ <li ><a href="#method-i-ref_count">#ref_count</a>
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+
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+ <li ><a href="#method-i-to_s">#to_s</a>
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+ <li ><a href="#method-i-to_vcf">#to_vcf</a>
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+
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+ </ul>
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+ </div>
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+
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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::Pileup">
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+ <h1 id="class-Bio::DB::Pileup" class="class">
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+ class Bio::DB::Pileup
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+ </h1>
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+
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+ <section class="description">
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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-ar1" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">ar1</span><span
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+ class="attribute-access-type">[RW]</span>
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+ <div id="attribute-i-ar2" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">ar2</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-ar3" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">ar3</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-consensus" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">consensus</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-consensus_quality" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">consensus_quality</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 id="attribute-i-coverage" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">coverage</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">indel_1</span><span
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+ class="attribute-access-type">[RW]</span>
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">indel_2</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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+ </div>
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+ </div>
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+ </div>
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+ <div id="attribute-i-read_bases" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">read_bases</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-read_quals" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">read_quals</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-ref_base" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">ref_base</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-ref_name" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">ref_name</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-rms_mapq" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">rms_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-snp_quality" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">snp_quality</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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+
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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-iupac_to_base" class="method-detail ">
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+
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+ <div class="method-heading">
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+ <span class="method-name">iupac_to_base</span><span
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+ class="method-args">(alt_base)</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>returns the two bases for the corresponding iupac code</p>
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+
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+
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+
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+ <div class="method-source-code" id="iupac_to_base-source">
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+ <pre><span class="ruby-comment"># File lib/bio/db/pileup.rb, line 177</span>
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+ <span class="ruby-keyword">def</span> <span class="ruby-constant">Pileup</span>.<span class="ruby-identifier">iupac_to_base</span>(<span class="ruby-identifier">alt_base</span>)
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+ <span class="ruby-keyword">case</span> <span class="ruby-identifier">alt_base</span>
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+ <span class="ruby-keyword">when</span> <span class="ruby-string">&#39;K&#39;</span> <span class="ruby-keyword">then</span> [<span class="ruby-string">&#39;G&#39;</span>,<span class="ruby-string">&#39;T&#39;</span>]
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+ <span class="ruby-keyword">when</span> <span class="ruby-string">&#39;M&#39;</span> <span class="ruby-keyword">then</span> [<span class="ruby-string">&#39;A&#39;</span>,<span class="ruby-string">&#39;C&#39;</span>]
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+ <span class="ruby-keyword">when</span> <span class="ruby-string">&#39;S&#39;</span> <span class="ruby-keyword">then</span> [<span class="ruby-string">&#39;C&#39;</span>,<span class="ruby-string">&#39;G&#39;</span>]
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+ <span class="ruby-keyword">when</span> <span class="ruby-string">&#39;R&#39;</span> <span class="ruby-keyword">then</span> [<span class="ruby-string">&#39;A&#39;</span>,<span class="ruby-string">&#39;G&#39;</span>]
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+ <span class="ruby-keyword">when</span> <span class="ruby-string">&#39;W&#39;</span> <span class="ruby-keyword">then</span> [<span class="ruby-string">&#39;A&#39;</span>,<span class="ruby-string">&#39;T&#39;</span>]
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+ <span class="ruby-keyword">when</span> <span class="ruby-string">&#39;Y&#39;</span> <span class="ruby-keyword">then</span> [<span class="ruby-string">&#39;C&#39;</span>,<span class="ruby-string">&#39;T&#39;</span>]
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+ <span class="ruby-keyword">else</span> <span class="ruby-identifier">alt_base</span>.<span class="ruby-identifier">split</span>(<span class="ruby-regexp">//</span>)
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+ <span class="ruby-keyword">end</span>
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+ <span class="ruby-keyword">end</span></pre>
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+ </div>
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+ </div>
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+ </div>
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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">(pile_up_line)</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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+ <div class="method-description">
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+
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+ <p>creates the <a href="Pileup.html">Pileup</a> object</p>
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+
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+ <pre>pile_up_line = &quot;seq2\t151\tG\tG\t36\t0\t99\t12\t...........A\t:9&lt;;;7=&lt;&lt;&lt;&lt;&lt;&quot;
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+ pile = Bio::DB::Pileup.new(pile_up_line)</pre>
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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/pileup.rb, line 35</span>
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+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">pile_up_line</span>)
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+ <span class="ruby-identifier">cols</span> = <span class="ruby-identifier">pile_up_line</span>.<span class="ruby-identifier">split</span>(<span class="ruby-regexp">/\t/</span>)
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+ <span class="ruby-keyword">if</span> <span class="ruby-identifier">cols</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">==</span> <span class="ruby-value">6</span> <span class="ruby-comment">##should only be able to get 6 lines from mpileup</span>
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+ <span class="ruby-ivar">@ref_name</span>, <span class="ruby-ivar">@pos</span>, <span class="ruby-ivar">@ref_base</span>, <span class="ruby-ivar">@coverage</span>, <span class="ruby-ivar">@read_bases</span>, <span class="ruby-ivar">@read_quals</span> = <span class="ruby-identifier">cols</span>
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+ <span class="ruby-keyword">elsif</span> (<span class="ruby-value">10</span><span class="ruby-operator">..</span><span class="ruby-value">13</span>).<span class="ruby-identifier">include?</span>(<span class="ruby-identifier">cols</span>.<span class="ruby-identifier">length</span>) <span class="ruby-comment">##incase anyone tries to use deprecated pileup with -c flag we get upto 13 cols...</span>
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+ <span class="ruby-keyword">if</span> <span class="ruby-identifier">cols</span>[<span class="ruby-value">2</span>] <span class="ruby-operator">==</span> <span class="ruby-string">&#39;*&#39;</span> <span class="ruby-comment">#indel</span>
401
+ <span class="ruby-ivar">@ref_name</span>, <span class="ruby-ivar">@pos</span>, <span class="ruby-ivar">@ref_base</span>, <span class="ruby-ivar">@consensus</span>, <span class="ruby-ivar">@consensus_quality</span>, <span class="ruby-ivar">@snp_quality</span>, <span class="ruby-ivar">@rms_mapq</span>, <span class="ruby-ivar">@coverage</span>, <span class="ruby-ivar">@indel_1</span>, <span class="ruby-ivar">@indel_2</span>, <span class="ruby-ivar">@ar1</span>, <span class="ruby-ivar">@ar2</span>, <span class="ruby-ivar">@ar3</span> = <span class="ruby-identifier">cols</span>
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+ <span class="ruby-keyword">else</span> <span class="ruby-comment">#snp / identity</span>
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+ <span class="ruby-ivar">@ref_name</span>, <span class="ruby-ivar">@pos</span>, <span class="ruby-ivar">@ref_base</span>, <span class="ruby-ivar">@consensus</span>, <span class="ruby-ivar">@consensus_quality</span>, <span class="ruby-ivar">@snp_quality</span>, <span class="ruby-ivar">@rms_mapq</span>, <span class="ruby-ivar">@coverage</span>, <span class="ruby-ivar">@read_bases</span>, <span class="ruby-ivar">@read_quals</span> = <span class="ruby-identifier">cols</span>
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+ <span class="ruby-keyword">end</span>
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+ <span class="ruby-ivar">@consensus_quality</span> = <span class="ruby-ivar">@consensus_quality</span>.<span class="ruby-identifier">to_f</span>
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+ <span class="ruby-ivar">@snp_quality</span> = <span class="ruby-ivar">@snp_quality</span>.<span class="ruby-identifier">to_f</span>
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+ <span class="ruby-ivar">@rms_mapq</span> = <span class="ruby-ivar">@rms_mapq</span>.<span class="ruby-identifier">to_f</span>
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+ <span class="ruby-keyword">else</span>
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+ <span class="ruby-comment">#raise RuntimeError, &quot;parsing line &#39;#{pile_up_line.chomp}&#39; failed&quot;</span>
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+ <span class="ruby-keyword">end</span>
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+
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+ <span class="ruby-ivar">@pos</span> = <span class="ruby-ivar">@pos</span>.<span class="ruby-identifier">to_i</span>
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+ <span class="ruby-ivar">@coverage</span> = <span class="ruby-ivar">@coverage</span>.<span class="ruby-identifier">to_f</span>
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+ <span class="ruby-ivar">@ref_count</span> = <span class="ruby-keyword">nil</span>
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+ <span class="ruby-ivar">@non_ref_count_hash</span> = <span class="ruby-keyword">nil</span>
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+ <span class="ruby-ivar">@non_ref_count</span> = <span class="ruby-keyword">nil</span>
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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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+
423
+
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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 id="public-instance-5Buntitled-5D-method-details" class="method-section">
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+ <header>
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+ <h3>Public Instance Methods</h3>
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+ </header>
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+
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+
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+ <div id="method-i-genotype_list" class="method-detail ">
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+
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+ <div class="method-heading">
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+ <span class="method-name">genotype_list</span><span
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+ class="method-args">()</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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+
449
+ <p>identifies the reference base and returns the indel or snp genotype as
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+ applicable</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="genotype_list-source">
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+ <pre><span class="ruby-comment"># File lib/bio/db/pileup.rb, line 167</span>
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+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">genotype_list</span>
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+ <span class="ruby-keyword">if</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">ref_base</span> <span class="ruby-operator">==</span> <span class="ruby-string">&#39;*&#39;</span>
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+ <span class="ruby-keyword">return</span> <span class="ruby-identifier">indel_gt</span>
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+ <span class="ruby-keyword">else</span>
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+ <span class="ruby-keyword">return</span> <span class="ruby-identifier">snp_gt</span>
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+ <span class="ruby-keyword">end</span>
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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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+ <div id="method-i-non_ref_count" class="method-detail ">
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+
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+ <div class="method-heading">
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+ <span class="method-name">non_ref_count</span><span
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+ class="method-args">()</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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+
487
+ <p>returns the total non-reference bases in the reads at this position</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="non_ref_count-source">
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+ <pre><span class="ruby-comment"># File lib/bio/db/pileup.rb, line 69</span>
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+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">non_ref_count</span>
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+ <span class="ruby-keyword">if</span> <span class="ruby-ivar">@non_ref_count</span>.<span class="ruby-identifier">nil?</span>
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+ <span class="ruby-ivar">@non_ref_count</span> = <span class="ruby-ivar">@read_bases</span>.<span class="ruby-identifier">count</span>(<span class="ruby-string">&quot;ATGCatgc&quot;</span>).<span class="ruby-identifier">to_f</span>
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+ <span class="ruby-keyword">end</span>
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+ <span class="ruby-ivar">@non_ref_count</span>
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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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+ <div id="method-i-non_refs" class="method-detail ">
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+
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+ <div class="method-heading">
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+ <span class="method-name">non_refs</span><span
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+ class="method-args">()</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>Calculate the total count of each non-reference nucleotide and return a
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+ hash of all 4 nt counts returns a hash pile.non_refs #{:A =&gt; 1, :C =&gt;
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+ 0, :T =&gt; 0, :G =&gt; 0}</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="non_refs-source">
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+ <pre><span class="ruby-comment"># File lib/bio/db/pileup.rb, line 61</span>
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+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">non_refs</span>
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+ <span class="ruby-keyword">if</span> <span class="ruby-ivar">@non_ref_count_hash</span>.<span class="ruby-identifier">nil?</span>
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+ <span class="ruby-ivar">@non_ref_count_hash</span> = {<span class="ruby-value">:A</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">read_bases</span>.<span class="ruby-identifier">count</span>(<span class="ruby-string">&quot;Aa&quot;</span>), <span class="ruby-value">:C</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">read_bases</span>.<span class="ruby-identifier">count</span>(<span class="ruby-string">&quot;Cc&quot;</span>), <span class="ruby-value">:G</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">read_bases</span>.<span class="ruby-identifier">count</span>(<span class="ruby-string">&quot;Gg&quot;</span>), <span class="ruby-value">:T</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">read_bases</span>.<span class="ruby-identifier">count</span>(<span class="ruby-string">&quot;Tt&quot;</span>)}
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+ <span class="ruby-keyword">end</span>
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+ <span class="ruby-ivar">@non_ref_count_hash</span>
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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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+
545
+ </div>
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+
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+
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+ <div id="method-i-parse_indel" class="method-detail ">
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+
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+ <div class="method-heading">
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+ <span class="method-name">parse_indel</span><span
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+ class="method-args">(alt)</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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+
559
+ <div class="method-description">
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+
561
+ <p>identifies if the indel is an insertion or a deletion</p>
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+
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+
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+
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+
566
+ <div class="method-source-code" id="parse_indel-source">
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+ <pre><span class="ruby-comment"># File lib/bio/db/pileup.rb, line 190</span>
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+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">parse_indel</span>(<span class="ruby-identifier">alt</span>)
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+ <span class="ruby-keyword">return</span> <span class="ruby-node">&quot;D#{$&#39;.length}&quot;</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">alt</span> <span class="ruby-operator">=~</span><span class="ruby-regexp">/^-/</span>
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+ <span class="ruby-keyword">if</span> <span class="ruby-identifier">alt</span><span class="ruby-operator">=~</span><span class="ruby-regexp">/^\+/</span>
571
+ <span class="ruby-keyword">return</span> <span class="ruby-node">&quot;I#{$&#39;}&quot;</span>
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+ <span class="ruby-keyword">elsif</span> <span class="ruby-identifier">alt</span> <span class="ruby-operator">==</span> <span class="ruby-string">&#39;*&#39;</span>
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+ <span class="ruby-keyword">return</span> <span class="ruby-keyword">nil</span>
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+ <span class="ruby-keyword">end</span>
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+ <span class="ruby-keyword">end</span></pre>
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+ </div>
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+
578
+ </div>
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+
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+
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+
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+
583
+ </div>
584
+
585
+
586
+ <div id="method-i-ref_count" class="method-detail ">
587
+
588
+ <div class="method-heading">
589
+ <span class="method-name">ref_count</span><span
590
+ class="method-args">()</span>
591
+
592
+ <span class="method-click-advice">click to toggle source</span>
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+
594
+ </div>
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+
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+
597
+ <div class="method-description">
598
+
599
+ <p>returns the count of reference-bases in the reads at this position</p>
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+
601
+
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+
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+
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+ <div class="method-source-code" id="ref_count-source">
605
+ <pre><span class="ruby-comment"># File lib/bio/db/pileup.rb, line 77</span>
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+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">ref_count</span>
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+ <span class="ruby-keyword">if</span> <span class="ruby-ivar">@ref_count</span>.<span class="ruby-identifier">nil?</span>
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+ <span class="ruby-ivar">@ref_count</span> = <span class="ruby-keyword">self</span>.<span class="ruby-identifier">read_bases</span>.<span class="ruby-identifier">count</span>(<span class="ruby-string">&quot;.,&quot;</span>)
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+ <span class="ruby-keyword">end</span>
610
+ <span class="ruby-ivar">@ref_count</span>
611
+ <span class="ruby-keyword">end</span></pre>
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+ </div>
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+
614
+ </div>
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+
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+
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+
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+
619
+ </div>
620
+
621
+
622
+ <div id="method-i-to_s" class="method-detail ">
623
+
624
+ <div class="method-heading">
625
+ <span class="method-name">to_s</span><span
626
+ class="method-args">()</span>
627
+
628
+ <span class="method-click-advice">click to toggle source</span>
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+
630
+ </div>
631
+
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+
633
+ <div class="method-description">
634
+
635
+ <p>returns pileup format line</p>
636
+
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+
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+
639
+
640
+ <div class="method-source-code" id="to_s-source">
641
+ <pre><span class="ruby-comment"># File lib/bio/db/pileup.rb, line 201</span>
642
+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">to_s</span>
643
+ <span class="ruby-keyword">if</span> <span class="ruby-ivar">@read_quals</span> <span class="ruby-keyword">and</span> <span class="ruby-operator">!</span><span class="ruby-ivar">@consensus_quality</span> <span class="ruby-comment">#6col</span>
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+ [<span class="ruby-ivar">@ref_name</span>, <span class="ruby-ivar">@pos</span>, <span class="ruby-ivar">@ref_base</span>, <span class="ruby-ivar">@coverage</span>.<span class="ruby-identifier">to_i</span>, <span class="ruby-ivar">@read_bases</span>, <span class="ruby-ivar">@read_quals</span>].<span class="ruby-identifier">join</span>(<span class="ruby-string">&quot;\t&quot;</span>)
645
+ <span class="ruby-keyword">elsif</span> <span class="ruby-ivar">@indel_1</span> <span class="ruby-comment">#13 cols</span>
646
+ [<span class="ruby-ivar">@ref_name</span>, <span class="ruby-ivar">@pos</span>, <span class="ruby-ivar">@ref_base</span>, <span class="ruby-ivar">@consensus</span>, <span class="ruby-ivar">@consensus_quality</span>.<span class="ruby-identifier">to_i</span>, <span class="ruby-ivar">@snp_quality</span>.<span class="ruby-identifier">to_i</span>, <span class="ruby-ivar">@rms_mapq</span>.<span class="ruby-identifier">to_i</span>, <span class="ruby-ivar">@coverage</span>.<span class="ruby-identifier">to_i</span>, <span class="ruby-ivar">@indel_1</span>, <span class="ruby-ivar">@indel_2</span>, <span class="ruby-ivar">@ar1</span>, <span class="ruby-ivar">@ar2</span>, <span class="ruby-ivar">@ar3</span>].<span class="ruby-identifier">join</span>(<span class="ruby-string">&quot;\t&quot;</span>)
647
+ <span class="ruby-keyword">else</span> <span class="ruby-comment">#10 cols</span>
648
+ [<span class="ruby-ivar">@ref_name</span>, <span class="ruby-ivar">@pos</span>, <span class="ruby-ivar">@ref_base</span>, <span class="ruby-ivar">@consensus</span>, <span class="ruby-ivar">@consensus_quality</span>.<span class="ruby-identifier">to_i</span>, <span class="ruby-ivar">@snp_quality</span>.<span class="ruby-identifier">to_i</span>, <span class="ruby-ivar">@rms_mapq</span>.<span class="ruby-identifier">to_i</span>, <span class="ruby-ivar">@coverage</span>.<span class="ruby-identifier">to_i</span>, <span class="ruby-ivar">@read_bases</span>, <span class="ruby-ivar">@read_quals</span>].<span class="ruby-identifier">join</span>(<span class="ruby-string">&quot;\t&quot;</span>)
649
+ <span class="ruby-keyword">end</span>
650
+
651
+ <span class="ruby-keyword">end</span></pre>
652
+ </div>
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+
654
+ </div>
655
+
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+
657
+
658
+
659
+ </div>
660
+
661
+
662
+ <div id="method-i-to_vcf" class="method-detail ">
663
+
664
+ <div class="method-heading">
665
+ <span class="method-name">to_vcf</span><span
666
+ class="method-args">()</span>
667
+
668
+ <span class="method-click-advice">click to toggle source</span>
669
+
670
+ </div>
671
+
672
+
673
+ <div class="method-description">
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+
675
+ <p>returns basic VCF string as per samtools/misc sam2vcf.pl except that it
676
+ scrimps on the ref for indels, returning a &#39;*&#39; instead of the
677
+ reference allele</p>
678
+
679
+
680
+
681
+
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+ <div class="method-source-code" id="to_vcf-source">
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+ <pre><span class="ruby-comment"># File lib/bio/db/pileup.rb, line 103</span>
684
+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">to_vcf</span>
685
+ <span class="ruby-identifier">alt</span>,<span class="ruby-identifier">g</span> = <span class="ruby-keyword">self</span>.<span class="ruby-identifier">genotype_list</span>
686
+ <span class="ruby-identifier">alt</span> = <span class="ruby-keyword">self</span>.<span class="ruby-identifier">consensus</span>.<span class="ruby-identifier">split</span>(<span class="ruby-regexp">//</span>).<span class="ruby-identifier">join</span>(<span class="ruby-string">&#39;,&#39;</span>) <span class="ruby-keyword">unless</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">ref_base</span> <span class="ruby-operator">==</span> <span class="ruby-string">&#39;*&#39;</span>
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+ <span class="ruby-identifier">alt</span> = <span class="ruby-string">&#39;.&#39;</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">alt</span> <span class="ruby-operator">==</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">ref_base</span>
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+ [<span class="ruby-keyword">self</span>.<span class="ruby-identifier">ref_name</span>, <span class="ruby-keyword">self</span>.<span class="ruby-identifier">pos</span>, <span class="ruby-string">&#39;.&#39;</span>, <span class="ruby-keyword">self</span>.<span class="ruby-identifier">ref_base</span>, <span class="ruby-identifier">alt</span>, <span class="ruby-keyword">self</span>.<span class="ruby-identifier">snp_quality</span>.<span class="ruby-identifier">to_i</span>, <span class="ruby-string">&quot;0&quot;</span>, <span class="ruby-node">&quot;DP=#{self.coverage.to_i}&quot;</span>, <span class="ruby-string">&quot;GT:GQ:DP&quot;</span>, <span class="ruby-node">&quot;#{g}:#{self.consensus_quality.to_i}:#{self.coverage.to_i}&quot;</span> ].<span class="ruby-identifier">join</span>(<span class="ruby-string">&quot;\t&quot;</span>)
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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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+
697
+ </div>
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+
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+
700
+ </section>
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+
702
+ </section>
703
+ </main>
704
+
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+
706
+ <footer id="validator-badges" role="contentinfo">
707
+ <p><a href="http://validator.w3.org/check/referer">Validate</a>
708
+ <p>Generated by <a href="http://rdoc.rubyforge.org">RDoc</a> 4.1.1.
709
+ <p>Based on <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish</a> by <a href="http://deveiate.org">Michael Granger</a>.
710
+ </footer>
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+