bio-samtools 0.4.1 → 0.4.2

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  1. data/VERSION +1 -1
  2. data/bio-samtools.gemspec +60 -6
  3. data/doc/Bio.html +171 -0
  4. data/doc/Bio/DB.html +163 -0
  5. data/doc/Bio/DB/Alignment.html +780 -0
  6. data/doc/Bio/DB/SAM.html +1241 -0
  7. data/doc/Bio/DB/SAM/Library.html +217 -0
  8. data/doc/Bio/DB/SAM/Tools.html +331 -0
  9. data/doc/Bio/DB/SAM/Tools/Bam1CoreT.html +159 -0
  10. data/doc/Bio/DB/SAM/Tools/Bam1T.html +220 -0
  11. data/doc/Bio/DB/SAM/Tools/BamHeaderT.html +249 -0
  12. data/doc/Bio/DB/SAM/Tools/BamPileup1T.html +159 -0
  13. data/doc/Bio/DB/SAM/Tools/SamfileT.html +171 -0
  14. data/doc/Bio/DB/SAM/Tools/SamfileTX.html +159 -0
  15. data/doc/Bio/DB/SAMException.html +205 -0
  16. data/doc/Bio/DB/Tag.html +254 -0
  17. data/doc/LICENSE_txt.html +881 -0
  18. data/doc/LibC.html +153 -0
  19. data/doc/Pileup.html +571 -0
  20. data/doc/Vcf.html +473 -0
  21. data/doc/created.rid +10 -1
  22. data/doc/images/add.png +0 -0
  23. data/doc/images/brick.png +0 -0
  24. data/doc/images/brick_link.png +0 -0
  25. data/doc/images/bug.png +0 -0
  26. data/doc/images/bullet_black.png +0 -0
  27. data/doc/images/bullet_toggle_minus.png +0 -0
  28. data/doc/images/bullet_toggle_plus.png +0 -0
  29. data/doc/images/date.png +0 -0
  30. data/doc/images/delete.png +0 -0
  31. data/doc/images/find.png +0 -0
  32. data/doc/images/loadingAnimation.gif +0 -0
  33. data/doc/images/macFFBgHack.png +0 -0
  34. data/doc/images/package.png +0 -0
  35. data/doc/images/page_green.png +0 -0
  36. data/doc/images/page_white_text.png +0 -0
  37. data/doc/images/page_white_width.png +0 -0
  38. data/doc/images/plugin.png +0 -0
  39. data/doc/images/ruby.png +0 -0
  40. data/doc/images/tag_blue.png +0 -0
  41. data/doc/images/tag_green.png +0 -0
  42. data/doc/images/transparent.png +0 -0
  43. data/doc/images/wrench.png +0 -0
  44. data/doc/images/wrench_orange.png +0 -0
  45. data/doc/images/zoom.png +0 -0
  46. data/doc/index.html +109 -21
  47. data/doc/js/darkfish.js +153 -0
  48. data/doc/js/jquery.js +18 -0
  49. data/doc/js/navigation.js +142 -0
  50. data/doc/js/search.js +94 -0
  51. data/doc/js/search_index.js +1 -0
  52. data/doc/js/searcher.js +228 -0
  53. data/doc/lib/bio-samtools_rb.html +115 -0
  54. data/doc/lib/bio/db/sam/bam_rb.html +121 -0
  55. data/doc/lib/bio/db/sam/faidx_rb.html +117 -0
  56. data/doc/lib/bio/db/sam/library_rb.html +115 -0
  57. data/doc/lib/bio/db/sam/pileup_rb.html +171 -0
  58. data/doc/lib/bio/db/sam/sam_rb.html +121 -0
  59. data/doc/lib/bio/db/sam/vcf_rb.html +124 -0
  60. data/doc/lib/bio/db/sam_rb.html +115 -0
  61. data/doc/rdoc.css +543 -0
  62. data/doc/table_of_contents.html +186 -0
  63. data/ext/Makefile-bioruby.patch +1 -1
  64. data/ext/Rakefile +8 -1
  65. data/ext/mkrf_conf.rb +8 -1
  66. data/lib/bio/db/sam.rb +140 -27
  67. data/lib/bio/db/sam/vcf.rb +0 -1
  68. data/test/basictest.rb +4 -4
  69. data/test/test_basic.rb +50 -34
  70. metadata +79 -25
  71. data/test/coverage.rb +0 -26
  72. data/test/coverage_plot.rb +0 -28
  73. data/test/feature.rb +0 -0
  74. data/test/test_pileup.rb +0 -68
data/doc/lib/bio/db/sam/faidx_rb.html ADDED
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+ <nav id="classindex-section" class="section project-section">
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+ <ul class="link-list">
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+ <li><a href="../../../../Bio.html">Bio</a>
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+ <li><a href="../../../../Bio/DB.html">Bio::DB</a>
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+ <li><a href="../../../../Bio/DB/Alignment.html">Bio::DB::Alignment</a>
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+ <li><a href="../../../../Bio/DB/SAM.html">Bio::DB::SAM</a>
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+ <li><a href="../../../../Bio/DB/SAM/Library.html">Bio::DB::SAM::Library</a>
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+ <li><a href="../../../../Bio/DB/SAM/Tools.html">Bio::DB::SAM::Tools</a>
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+ <li><a href="../../../../Bio/DB/SAM/Tools/Bam1CoreT.html">Bio::DB::SAM::Tools::Bam1CoreT</a>
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+
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+ <li><a href="../../../../Bio/DB/SAM/Tools/Bam1T.html">Bio::DB::SAM::Tools::Bam1T</a>
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+
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+ <li><a href="../../../../Bio/DB/SAM/Tools/BamHeaderT.html">Bio::DB::SAM::Tools::BamHeaderT</a>
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+
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+ <li><a href="../../../../Bio/DB/SAM/Tools/BamPileup1T.html">Bio::DB::SAM::Tools::BamPileup1T</a>
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+
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+ <li><a href="../../../../Bio/DB/SAM/Tools/SamfileT.html">Bio::DB::SAM::Tools::SamfileT</a>
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+
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+ <li><a href="../../../../Bio/DB/SAM/Tools/SamfileTX.html">Bio::DB::SAM::Tools::SamfileTX</a>
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+
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+ <li><a href="../../../../Bio/DB/SAMException.html">Bio::DB::SAMException</a>
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+
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+ <li><a href="../../../../Bio/DB/Sam.html">Bio::DB::Sam</a>
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+
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+ <li><a href="../../../../Bio/DB/Tag.html">Bio::DB::Tag</a>
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+
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+ <li><a href="../../../../LibC.html">LibC</a>
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+
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+ <li><a href="../../../../Pileup.html">Pileup</a>
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+ <li><a href="../../../../Vcf.html">Vcf</a>
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+ </ul>
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+ </nav>
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+ </div>
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+ </nav>
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+
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+ <div id="documentation" class="description">
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+
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+ <p>require ‘rubygems’ require’ffi’ require ‘bio/db/sam/bam’</p>
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+ </div>
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data/doc/lib/bio/db/sam/library_rb.html ADDED
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+ <nav id="classindex-section" class="section project-section">
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+ <li><a href="../../../../Bio.html">Bio</a>
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+ <li><a href="../../../../Bio/DB.html">Bio::DB</a>
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+ <li><a href="../../../../Bio/DB/Alignment.html">Bio::DB::Alignment</a>
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+ <li><a href="../../../../Bio/DB/SAM.html">Bio::DB::SAM</a>
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+ <li><a href="../../../../Bio/DB/SAM/Library.html">Bio::DB::SAM::Library</a>
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+ <li><a href="../../../../Bio/DB/SAM/Tools.html">Bio::DB::SAM::Tools</a>
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+ <li><a href="../../../../Bio/DB/SAM/Tools/Bam1CoreT.html">Bio::DB::SAM::Tools::Bam1CoreT</a>
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+ <li><a href="../../../../Bio/DB/SAM/Tools/Bam1T.html">Bio::DB::SAM::Tools::Bam1T</a>
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+ <li><a href="../../../../Bio/DB/SAM/Tools/BamHeaderT.html">Bio::DB::SAM::Tools::BamHeaderT</a>
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+ <li><a href="../../../../Bio/DB/SAM/Tools/BamPileup1T.html">Bio::DB::SAM::Tools::BamPileup1T</a>
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+ <li><a href="../../../../Bio/DB/SAM/Tools/SamfileT.html">Bio::DB::SAM::Tools::SamfileT</a>
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+ <li><a href="../../../../Bio/DB/SAM/Tools/SamfileTX.html">Bio::DB::SAM::Tools::SamfileTX</a>
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+ <li><a href="../../../../LibC.html">LibC</a>
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+ <li><a href="../../../../Pileup.html">Pileup</a>
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data/doc/lib/bio/db/sam/pileup_rb.html ADDED
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+ <!DOCTYPE html>
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+ </nav>
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+ <nav id="classindex-section" class="section project-section">
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+ <h3 class="section-header">Class and Module Index</h3>
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+ <ul class="link-list">
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+ <li><a href="../../../../Bio.html">Bio</a>
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+ <li><a href="../../../../Bio/DB.html">Bio::DB</a>
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+ <li><a href="../../../../Bio/DB/Alignment.html">Bio::DB::Alignment</a>
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+ <li><a href="../../../../Bio/DB/SAM.html">Bio::DB::SAM</a>
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+ <li><a href="../../../../Bio/DB/SAM/Library.html">Bio::DB::SAM::Library</a>
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+ <li><a href="../../../../Bio/DB/SAM/Tools.html">Bio::DB::SAM::Tools</a>
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+ <li><a href="../../../../Bio/DB/SAM/Tools/Bam1CoreT.html">Bio::DB::SAM::Tools::Bam1CoreT</a>
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+
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+ <li><a href="../../../../Bio/DB/SAM/Tools/Bam1T.html">Bio::DB::SAM::Tools::Bam1T</a>
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+
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+ <li><a href="../../../../Bio/DB/SAM/Tools/BamHeaderT.html">Bio::DB::SAM::Tools::BamHeaderT</a>
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+
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+ <li><a href="../../../../Bio/DB/SAM/Tools/BamPileup1T.html">Bio::DB::SAM::Tools::BamPileup1T</a>
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+
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+ <li><a href="../../../../Bio/DB/SAM/Tools/SamfileT.html">Bio::DB::SAM::Tools::SamfileT</a>
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+
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+ <li><a href="../../../../Bio/DB/SAM/Tools/SamfileTX.html">Bio::DB::SAM::Tools::SamfileTX</a>
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+
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+ <li><a href="../../../../Bio/DB/SAMException.html">Bio::DB::SAMException</a>
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+ <li><a href="../../../../Bio/DB/Sam.html">Bio::DB::Sam</a>
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+ <li><a href="../../../../Bio/DB/Tag.html">Bio::DB::Tag</a>
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+
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+ <li><a href="../../../../LibC.html">LibC</a>
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+ <li><a href="../../../../Pileup.html">Pileup</a>
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+ <li><a href="../../../../Vcf.html">Vcf</a>
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+ </ul>
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+ </nav>
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+
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+ </div>
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+ </nav>
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+
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+ <div id="documentation" class="description">
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+
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+ <h1 id="label-Pileup+"><a href="../../../../Pileup.html">Pileup</a> </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 (tsl at dan.maclean.ac.uk)</p>
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+ </dd></dl>
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+
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+ <p><a href="../../../../Pileup.html">Pileup</a> 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 `*‘ 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’.</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’. Suppose the reference base
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+ 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’, indel lines and columns between 3 and
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+ 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;”
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+ <a href="../../../../Pileup.html">Pileup</a> provides accessors for all
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+ columns (6 or 10 column format) and a few other useful methods</p>
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+
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+ </div>
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+
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+
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+ <pre>sam.rb
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+ Created by Ricardo Ramirez on 3/25/10.</pre>
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+ <p>require ‘rubygems’ require’ffi’ require ‘bio/db/sam/bam’</p>
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