bio-samtools-wrapper 2.7.0

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  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
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  17. data/doc/Bio/DB/Vcf.html +431 -0
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  19. data/doc/Bio.html +175 -0
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  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
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  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.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</title>
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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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+ </div>
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+ </nav>
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+
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+ <main role="main" aria-labelledby="class-Bio::DB">
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+ <h1 id="class-Bio::DB" class="class">
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+ class Bio::DB
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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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+
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+ </section>
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+ </main>
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+ </footer>
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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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+ <title>module Bio - Pileup</title>
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+ type="text" name="search" placeholder="Search" spellcheck="false"
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+ <div class="nav-section">
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+ <h3>Table of Contents</h3>
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+
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+ <ul class="link-list" role="directory">
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+ <li><a href="#module-Bio-label-Bio%3A%3ADB%3A%3APileup+">Bio::DB::Pileup </a>
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+ <li><a href="#module-Bio-label-Vcf+">Vcf </a>
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+ </ul>
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+ </div>
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+
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+ <div id="class-metadata">
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+ </div>
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+ </nav>
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+ <main role="main" aria-labelledby="module-Bio">
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+ <h1 id="module-Bio" class="module">
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+ module Bio
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+ </h1>
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+
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+ <section class="description">
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+
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+ <h1 id="module-Bio-label-Bio%3A%3ADB%3A%3APileup+"><a href="Bio/DB/Pileup.html">Bio::DB::Pileup</a> <span><a href="#module-Bio-label-Bio%3A%3ADB%3A%3APileup+">&para;</a> <a href="#documentation">&uarr;</a></span></h1>
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+
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+ <p>A class representing information in SAMTools pileup format</p>
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+ <dl class="rdoc-list note-list"><dt>Author
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+ <dd>
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+ <p>Dan MacLean (dan.maclean@tsl.ac.uk)</p>
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+ </dd></dl>
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+
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+ <p>Pileup is described at <a
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+ href="http://sourceforge.net/apps/mediawiki/samtools/index.php?title=SAM_FAQ#I_do_not_understand_the_columns_in_the_pileup_output">sourceforge.net/apps/mediawiki/samtools/index.php?title=SAM_FAQ#I_do_not_understand_the_columns_in_the_pileup_output</a>.
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+ Briefly (when you invoke pileup with the -c option):</p>
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+ <ul><li>
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+ <p>1 reference sequence name</p>
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+ </li><li>
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+ <p>2 reference coordinate</p>
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+ </li><li>
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+ <p>(3) reference base, or `*&#39; for an indel line</p>
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+ </li><li>
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+ <p>(4) genotype where heterozygotes are encoded in the IUB code: M=A/C, R=A/G,
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+ W=A/T, S=C/G, Y=C/T and K=G/T; indels are indicated by, for example, +A,
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+ -A or +CC/-C. There is no difference between */+A or +A/*.</p>
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+ </li><li>
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+ <p>(5) Phred-scaled likelihood that the genotype is wrong, which is also
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+ called `consensus quality&#39;.</p>
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+ </li><li>
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+ <p>(6) Phred-scaled likelihood that the genotype is identical to the
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+ reference, which is also called `SNP quality&#39;. Suppose the reference
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+ base is A and in alignment we see 17 G and 3 A. We will get a low consensus
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+ quality because it is difficult to distinguish an A/G heterozygote from a
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+ G/G homozygote. We will get a high SNP quality, though, because the
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+ evidence of a SNP is very strong.</p>
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+ </li><li>
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+ <p>(7) root mean square (RMS) mapping quality</p>
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+ </li><li>
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+ <p>8 # reads covering the position</p>
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+ </li><li>
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+ <p>9 read bases at a SNP line (check the manual page for more information);
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+ the 1st indel allele otherwise</p>
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+ </li><li>
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+ <p>10 base quality at a SNP line; the 2nd indel allele otherwise</p>
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+ </li><li>
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+ <p>(11) indel line only: # reads directly supporting the 1st indel allele</p>
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+ </li><li>
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+ <p>(12) indel line only: # reads directly supporting the 2nd indel allele</p>
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+ </li><li>
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+ <p>(13) indel line only: # reads supporting a third indel allele</p>
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+ </li></ul>
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+
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+ <p>If pileup is invoked without `-c&#39;, indel lines and columns between 3
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+ and 7 inclusive will not be outputted.</p>
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+
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+ <p>NB mpileup uses the 6 column output format eg
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+ “seq2t151tGtGt36t0t99t12t.….……At:9&lt;;;7=&lt;&lt;&lt;&lt;&lt;” Pileup
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+ provides accessors for all columns (6 or 10 column format) and a few other
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+ useful methods</p>
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+
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+ <p>require &#39;rubygems&#39; require&#39;ffi&#39; require
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+ &#39;bio/db/sam/bam&#39;</p>
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+
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+ <h1 id="module-Bio-label-Vcf+">Vcf <span><a href="#module-Bio-label-Vcf+">&para;</a> <a href="#documentation">&uarr;</a></span></h1>
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+
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+ <p>A class representing information in Variant Call Format Forked from vcfruby
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+ at <a
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+ href="https://github.com/jesserod/vcfruby">github.com/jesserod/vcfruby</a>
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+ Modified and tests written by Dan MacLean (dan.maclean@tsl.ac.uk) VCF is
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+ described at <a
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+ href="http://www.1000genomes.org/node/101">www.1000genomes.org/node/101</a></p>
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+
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+ </section>
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+ </main>
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