bio-samtools 0.2.5 → 0.3.0

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Files changed (73) hide show
  1. data/README.rdoc +7 -20
  2. data/Rakefile +11 -0
  3. data/VERSION +1 -1
  4. data/bio-samtools.gemspec +67 -1
  5. data/doc/basic_styles.css +31 -0
  6. data/doc/classes/Bio.html +139 -0
  7. data/doc/classes/Bio/DB.html +137 -0
  8. data/doc/classes/Bio/DB/Alignment.html +441 -0
  9. data/doc/classes/Bio/DB/Alignment.src/M000012.html +19 -0
  10. data/doc/classes/Bio/DB/Alignment.src/M000013.html +27 -0
  11. data/doc/classes/Bio/DB/Alignment.src/M000014.html +45 -0
  12. data/doc/classes/Bio/DB/Alignment.src/M000015.html +40 -0
  13. data/doc/classes/Bio/DB/SAM.html +510 -0
  14. data/doc/classes/Bio/DB/SAM/Library.html +135 -0
  15. data/doc/classes/Bio/DB/SAM/Library.src/M000006.html +28 -0
  16. data/doc/classes/Bio/DB/SAM/Tools.html +278 -0
  17. data/doc/classes/Bio/DB/SAM/Tools.src/M000007.html +20 -0
  18. data/doc/classes/Bio/DB/SAM/Tools/Bam1CoreT.html +111 -0
  19. data/doc/classes/Bio/DB/SAM/Tools/Bam1T.html +150 -0
  20. data/doc/classes/Bio/DB/SAM/Tools/Bam1T.src/M000010.html +20 -0
  21. data/doc/classes/Bio/DB/SAM/Tools/BamHeaderT.html +169 -0
  22. data/doc/classes/Bio/DB/SAM/Tools/BamHeaderT.src/M000008.html +19 -0
  23. data/doc/classes/Bio/DB/SAM/Tools/BamHeaderT.src/M000009.html +18 -0
  24. data/doc/classes/Bio/DB/SAM/Tools/BamPileup1T.html +111 -0
  25. data/doc/classes/Bio/DB/SAM/Tools/SamfileT.html +129 -0
  26. data/doc/classes/Bio/DB/SAM/Tools/SamfileTX.html +111 -0
  27. data/doc/classes/Bio/DB/SAMException.html +140 -0
  28. data/doc/classes/Bio/DB/SAMException.src/M000016.html +18 -0
  29. data/doc/classes/Bio/DB/Sam.src/M000017.html +43 -0
  30. data/doc/classes/Bio/DB/Sam.src/M000018.html +42 -0
  31. data/doc/classes/Bio/DB/Sam.src/M000019.html +18 -0
  32. data/doc/classes/Bio/DB/Sam.src/M000020.html +22 -0
  33. data/doc/classes/Bio/DB/Sam.src/M000021.html +19 -0
  34. data/doc/classes/Bio/DB/Sam.src/M000022.html +25 -0
  35. data/doc/classes/Bio/DB/Sam.src/M000023.html +28 -0
  36. data/doc/classes/Bio/DB/Sam.src/M000024.html +28 -0
  37. data/doc/classes/Bio/DB/Sam.src/M000025.html +46 -0
  38. data/doc/classes/Bio/DB/Sam.src/M000026.html +24 -0
  39. data/doc/classes/Bio/DB/Sam.src/M000027.html +19 -0
  40. data/doc/classes/Bio/DB/Sam.src/M000028.html +24 -0
  41. data/doc/classes/Bio/DB/Sam.src/M000029.html +41 -0
  42. data/doc/classes/Bio/DB/Sam.src/M000030.html +31 -0
  43. data/doc/classes/Bio/DB/Sam.src/M000031.html +86 -0
  44. data/doc/classes/Bio/DB/Sam.src/M000032.html +34 -0
  45. data/doc/classes/Bio/DB/Tag.html +160 -0
  46. data/doc/classes/Bio/DB/Tag.src/M000011.html +21 -0
  47. data/doc/classes/LibC.html +105 -0
  48. data/doc/classes/Pileup.html +374 -0
  49. data/doc/classes/Pileup.src/M000001.html +34 -0
  50. data/doc/classes/Pileup.src/M000002.html +21 -0
  51. data/doc/classes/Pileup.src/M000003.html +21 -0
  52. data/doc/classes/Pileup.src/M000004.html +21 -0
  53. data/doc/classes/Pileup.src/M000005.html +31 -0
  54. data/doc/created.rid +1 -0
  55. data/doc/files/lib/bio-samtools_rb.html +109 -0
  56. data/doc/files/lib/bio/db/sam/bam_rb.html +108 -0
  57. data/doc/files/lib/bio/db/sam/faidx_rb.html +108 -0
  58. data/doc/files/lib/bio/db/sam/library_rb.html +101 -0
  59. data/doc/files/lib/bio/db/sam/pileup_rb.html +178 -0
  60. data/doc/files/lib/bio/db/sam/sam_rb.html +113 -0
  61. data/doc/files/lib/bio/db/sam_rb.html +111 -0
  62. data/doc/fr_class_index.html +43 -0
  63. data/doc/fr_file_index.html +33 -0
  64. data/doc/fr_method_index.html +58 -0
  65. data/doc/index.html +24 -0
  66. data/doc/rdoc-style.css +208 -0
  67. data/doc/tutorial.html +165 -0
  68. data/doc/tutorial.pdf +0 -0
  69. data/lib/bio/db/sam.rb +163 -1
  70. data/lib/bio/db/sam/pileup.rb +98 -0
  71. data/test/basictest.rb +14 -0
  72. data/test/pileup.rb +68 -0
  73. metadata +84 -18
data/doc/classes/Bio/DB/Alignment.html ADDED
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+ <head>
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+ <title>Class: Bio::DB::Alignment</title>
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+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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+ <meta http-equiv="Content-Script-Type" content="text/javascript" />
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+ <link rel="stylesheet" href="../../.././rdoc-style.css" type="text/css" media="screen" />
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+ <table class="header-table">
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+ <td><strong>Class</strong></td>
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+ <td class="class-name-in-header">Bio::DB::Alignment</td>
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+ </tr>
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+ <tr class="top-aligned-row">
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+ <td><strong>In:</strong></td>
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+ <td>
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+ <a href="../../../files/lib/bio/db/sam_rb.html">
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+ lib/bio/db/sam.rb
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+ </a>
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+ <br />
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+ </td>
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+ </tr>
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+
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+ <tr class="top-aligned-row">
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+ <td><strong>Parent:</strong></td>
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+ Object
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+ </table>
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+ </div>
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+
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+ <div id="method-list">
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+ <h3 class="section-bar">Methods</h3>
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+
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+ <div class="name-list">
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+ <a href="#M000013">finalize</a>&nbsp;&nbsp;
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+ <a href="#M000012">new</a>&nbsp;&nbsp;
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+ <a href="#M000015">sam=</a>&nbsp;&nbsp;
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+ <a href="#M000014">set</a>&nbsp;&nbsp;
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+ </div>
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+ </div>
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+
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+ </div>
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+ <h3 class="section-bar">Attributes</h3>
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+
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+ <div class="name-list">
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+ <table>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">al</td>
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+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
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+ <td class="context-item-desc">
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+ Attributes from the format
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+
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+ </td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">calend</td>
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+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
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+ <td class="context-item-desc">
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+ Attributes pulled with the C library
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+
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+ </td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">cigar</td>
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+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
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+ <td class="context-item-desc">
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+ Attributes from the format
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+
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+ </td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">failed_quality</td>
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+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
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+ <td class="context-item-desc">
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+ Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
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+ documentation) query_strand and mate_strand are true if they are forward.
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+ It is the opposite to the definition in the BAM format for clarity. primary
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+ is the negation of is_negative from the BAM format
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+
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+ </td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">first_in_pair</td>
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+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
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+ <td class="context-item-desc">
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+ Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
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+ documentation) query_strand and mate_strand are true if they are forward.
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+ It is the opposite to the definition in the BAM format for clarity. primary
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+ is the negation of is_negative from the BAM format
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+
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+ </td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">flag</td>
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+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
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+ <td class="context-item-desc">
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+ Attributes from the format
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+
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+ </td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">is_duplicate</td>
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+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
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+ <td class="context-item-desc">
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+ Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
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+ documentation) query_strand and mate_strand are true if they are forward.
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+ It is the opposite to the definition in the BAM format for clarity. primary
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+ is the negation of is_negative from the BAM format
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+
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+ </td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">is_mapped</td>
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+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
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+ <td class="context-item-desc">
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+ Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
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+ documentation) query_strand and mate_strand are true if they are forward.
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+ It is the opposite to the definition in the BAM format for clarity. primary
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+ is the negation of is_negative from the BAM format
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+
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+ </td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">is_paired</td>
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+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
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+ <td class="context-item-desc">
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+ Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
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+ documentation) query_strand and mate_strand are true if they are forward.
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+ It is the opposite to the definition in the BAM format for clarity. primary
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+ is the negation of is_negative from the BAM format
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+
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+ </td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">isize</td>
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+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
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+ <td class="context-item-desc">
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+ Attributes from the format
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+
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+ </td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">mapq</td>
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+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
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+ <td class="context-item-desc">
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+ Attributes from the format
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+
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+ </td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">mate_strand</td>
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+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
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+ <td class="context-item-desc">
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+ Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
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+ documentation) query_strand and mate_strand are true if they are forward.
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+ It is the opposite to the definition in the BAM format for clarity. primary
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+ is the negation of is_negative from the BAM format
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+
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+ </td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">mate_unmapped</td>
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+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
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+ <td class="context-item-desc">
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+ Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
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+ documentation) query_strand and mate_strand are true if they are forward.
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+ It is the opposite to the definition in the BAM format for clarity. primary
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+ is the negation of is_negative from the BAM format
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+
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+ </td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">mpos</td>
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+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
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+ <td class="context-item-desc">
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+ Attributes from the format
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+
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+ </td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">mrnm</td>
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+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
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+ <td class="context-item-desc">
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+ Attributes from the format
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+
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+ </td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">pos</td>
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+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
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+ <td class="context-item-desc">
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+ Attributes from the format
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+
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+ </td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">primary</td>
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+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
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+ <td class="context-item-desc">
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+ Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
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+ documentation) query_strand and mate_strand are true if they are forward.
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+ It is the opposite to the definition in the BAM format for clarity. primary
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+ is the negation of is_negative from the BAM format
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+
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+ </td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">qlen</td>
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+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
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+ <td class="context-item-desc">
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+ Attributes pulled with the C library
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+
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+ </td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">qname</td>
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+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
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+ <td class="context-item-desc">
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+ Attributes from the format
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+
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+ </td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">qual</td>
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+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
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+ <td class="context-item-desc">
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+ Attributes from the format
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+
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+ </td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">query_strand</td>
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+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
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+ <td class="context-item-desc">
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+ Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
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+ documentation) query_strand and mate_strand are true if they are forward.
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+ It is the opposite to the definition in the BAM format for clarity. primary
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+ is the negation of is_negative from the BAM format
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+
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+ </td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">query_unmapped</td>
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+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
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+ <td class="context-item-desc">
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+ Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
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+ documentation) query_strand and mate_strand are true if they are forward.
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+ It is the opposite to the definition in the BAM format for clarity. primary
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+ is the negation of is_negative from the BAM format
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+
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+ </td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">rname</td>
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+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
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+ <td class="context-item-desc">
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+ Attributes from the format
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+
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+ </td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">samstr</td>
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+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
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+ <td class="context-item-desc">
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+ Attributes from the format
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+
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+ </td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">second_in_pair</td>
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+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
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+ <td class="context-item-desc">
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+ Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
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+ documentation) query_strand and mate_strand are true if they are forward.
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+ It is the opposite to the definition in the BAM format for clarity. primary
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+ is the negation of is_negative from the BAM format
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+
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+ </td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">seq</td>
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+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
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+ <td class="context-item-desc">
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+ Attributes from the format
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+
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+ </td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">tags</td>
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+ <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
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+ <td class="context-item-desc">
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+ Attributes from the format
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+
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+ </td>
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+ </tr>
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+ </table>
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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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+ <!-- if method_list -->
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+ <div id="methods">
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+ <h3 class="section-bar">Public Class methods</h3>
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+
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+ <div id="method-M000013" class="method-detail">
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+ <a name="M000013"></a>
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+
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+ <div class="method-heading">
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+ <a href="Alignment.src/M000013.html" target="Code" class="method-signature"
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+ onclick="popupCode('Alignment.src/M000013.html');return false;">
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+ <span class="method-name">finalize</span><span class="method-args">(object_id)</span>
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+ </a>
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+ </div>
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+
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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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+ <div id="method-M000012" class="method-detail">
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+ <a name="M000012"></a>
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+
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+ <div class="method-heading">
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+ <a href="Alignment.src/M000012.html" target="Code" class="method-signature"
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+ onclick="popupCode('Alignment.src/M000012.html');return false;">
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+ <span class="method-name">new</span><span class="method-args">()</span>
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+ </a>
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+ </div>
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+
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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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+ <h3 class="section-bar">Public Instance methods</h3>
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+
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+ <div id="method-M000015" class="method-detail">
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+ <a name="M000015"></a>
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+
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+ <div class="method-heading">
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+ <a href="Alignment.src/M000015.html" target="Code" class="method-signature"
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+ onclick="popupCode('Alignment.src/M000015.html');return false;">
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+ <span class="method-name">sam=</span><span class="method-args">(sam)</span>
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+ </a>
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+ </div>
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+
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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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+ <div id="method-M000014" class="method-detail">
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+ <a name="M000014"></a>
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+
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+ <div class="method-heading">
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+ <a href="Alignment.src/M000014.html" target="Code" class="method-signature"
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+ onclick="popupCode('Alignment.src/M000014.html');return false;">
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+ <span class="method-name">set</span><span class="method-args">(bam_alignment, header)</span>
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+ </a>
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+ </div>
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+
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+ <div class="method-description">
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+ </div>
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+ </div>
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+ </div>
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+
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+
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+ <div id="validator-badges">
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+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
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+ </div>
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+
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+ </body>
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+ </html>
data/doc/classes/Bio/DB/Alignment.src/M000012.html ADDED
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
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+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+ <html>
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+ <head>
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+ <title>new (Bio::DB::Alignment)</title>
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+ <link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
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+ </head>
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+ <body class="standalone-code">
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+ <pre><span class="ruby-comment cmt"># File lib/bio/db/sam.rb, line 391</span>
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+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>
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+ <span class="ruby-constant">ObjectSpace</span>.<span class="ruby-identifier">define_finalizer</span>(<span class="ruby-keyword kw">self</span>,
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+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">class</span>.<span class="ruby-identifier">method</span>(<span class="ruby-identifier">:finalize</span>).<span class="ruby-identifier">to_proc</span>)
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+ <span class="ruby-keyword kw">end</span></pre>
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+ </html>