bio-samtools 0.6.2 → 2.0.3

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Files changed (160) hide show
  1. checksums.yaml +4 -4
  2. data/Gemfile +3 -2
  3. data/README.md +4 -7
  4. data/VERSION +1 -1
  5. data/bio-samtools.gemspec +47 -105
  6. data/doc/Bio.html +68 -131
  7. data/doc/Bio/DB.html +51 -111
  8. data/doc/Bio/DB/Alignment.html +135 -363
  9. data/doc/Bio/DB/Pileup.html +183 -170
  10. data/doc/Bio/DB/SAM.html +1396 -820
  11. data/doc/Bio/DB/SAM/Library.html +73 -123
  12. data/doc/Bio/DB/SAM/Tools.html +51 -273
  13. data/doc/Bio/DB/Tag.html +78 -124
  14. data/doc/Bio/DB/Vcf.html +111 -147
  15. data/doc/LICENSE_txt.html +113 -148
  16. data/doc/created.rid +9 -10
  17. data/doc/fonts.css +167 -0
  18. data/doc/fonts/Lato-Light.ttf +0 -0
  19. data/doc/fonts/Lato-LightItalic.ttf +0 -0
  20. data/doc/fonts/Lato-Regular.ttf +0 -0
  21. data/doc/fonts/Lato-RegularItalic.ttf +0 -0
  22. data/doc/fonts/SourceCodePro-Bold.ttf +0 -0
  23. data/doc/fonts/SourceCodePro-Regular.ttf +0 -0
  24. data/doc/images/add.png +0 -0
  25. data/doc/images/arrow_up.png +0 -0
  26. data/doc/images/delete.png +0 -0
  27. data/doc/images/tag_blue.png +0 -0
  28. data/doc/index.html +48 -54
  29. data/doc/js/darkfish.js +9 -22
  30. data/doc/js/search.js +20 -5
  31. data/doc/js/search_index.js +1 -1
  32. data/doc/rdoc.css +255 -218
  33. data/doc/table_of_contents.html +256 -137
  34. data/ext/Rakefile +57 -0
  35. data/lib/bio-samtools.rb +7 -2
  36. data/lib/bio/BIOExtensions.rb +89 -0
  37. data/lib/bio/db/alignment.rb +59 -0
  38. data/lib/bio/db/fastadb.rb +255 -0
  39. data/lib/bio/db/pileup.rb +221 -172
  40. data/lib/bio/db/sam.rb +639 -589
  41. data/lib/bio/db/sam/{faidx.rb → faidx_old.rb} +0 -0
  42. data/lib/bio/db/vcf.rb +69 -68
  43. data/test/.gitignore +1 -0
  44. data/test/{test_basic.rb → old_test_basic.rb} +33 -1
  45. data/test/samples/small/dupes.bam +0 -0
  46. data/test/samples/small/dupes.sam +274 -0
  47. data/test/samples/small/map_for_reheader.sam +8 -0
  48. data/test/samples/small/map_to_merge1.bam +0 -0
  49. data/test/samples/small/map_to_merge1.bam.bai +0 -0
  50. data/test/samples/small/map_to_merge1.sam +8 -0
  51. data/test/samples/small/map_to_merge2.bam +0 -0
  52. data/test/samples/small/map_to_merge2.bam.bai +0 -0
  53. data/test/samples/small/map_to_merge2.sam +8 -0
  54. data/test/samples/small/no_md.sam +8 -0
  55. data/test/samples/small/test_chr.fasta.1.bt2 +0 -0
  56. data/test/samples/small/test_chr.fasta.2.bt2 +0 -0
  57. data/test/samples/small/test_chr.fasta.3.bt2 +0 -0
  58. data/test/samples/small/test_chr.fasta.4.bt2 +0 -0
  59. data/test/samples/small/test_chr.fasta.rev.1.bt2 +0 -0
  60. data/test/samples/small/test_chr.fasta.rev.2.bt2 +0 -0
  61. data/test/samples/small/test_cov.svg +273 -0
  62. data/test/samples/small/testu.bam.bai +0 -0
  63. data/test/svg +133 -0
  64. data/test/test_pileup.rb +84 -0
  65. data/test/test_sam.rb +331 -0
  66. data/test/test_vcf.rb +11 -0
  67. data/{doc → tutorial}/tutorial.html +0 -0
  68. data/{doc → tutorial}/tutorial.pdf +0 -0
  69. metadata +56 -114
  70. data/doc/Bio/DB/SAM/Tools/Bam1CoreT.html +0 -159
  71. data/doc/Bio/DB/SAM/Tools/Bam1T.html +0 -220
  72. data/doc/Bio/DB/SAM/Tools/BamHeaderT.html +0 -249
  73. data/doc/Bio/DB/SAM/Tools/BamPileup1T.html +0 -159
  74. data/doc/Bio/DB/SAM/Tools/SamfileT.html +0 -171
  75. data/doc/Bio/DB/SAM/Tools/SamfileTX.html +0 -159
  76. data/doc/Bio/DB/SAMException.html +0 -205
  77. data/doc/LibC.html +0 -155
  78. data/doc/Pileup.html +0 -571
  79. data/doc/Vcf.html +0 -473
  80. data/doc/basic_styles.css +0 -31
  81. data/doc/classes/Bio.html +0 -139
  82. data/doc/classes/Bio/DB.html +0 -137
  83. data/doc/classes/Bio/DB/Alignment.html +0 -441
  84. data/doc/classes/Bio/DB/Alignment.src/M000012.html +0 -19
  85. data/doc/classes/Bio/DB/Alignment.src/M000013.html +0 -27
  86. data/doc/classes/Bio/DB/Alignment.src/M000014.html +0 -45
  87. data/doc/classes/Bio/DB/Alignment.src/M000015.html +0 -40
  88. data/doc/classes/Bio/DB/SAM.html +0 -510
  89. data/doc/classes/Bio/DB/SAM/Library.html +0 -135
  90. data/doc/classes/Bio/DB/SAM/Library.src/M000006.html +0 -28
  91. data/doc/classes/Bio/DB/SAM/Tools.html +0 -278
  92. data/doc/classes/Bio/DB/SAM/Tools.src/M000007.html +0 -20
  93. data/doc/classes/Bio/DB/SAM/Tools/Bam1CoreT.html +0 -111
  94. data/doc/classes/Bio/DB/SAM/Tools/Bam1T.html +0 -150
  95. data/doc/classes/Bio/DB/SAM/Tools/Bam1T.src/M000010.html +0 -20
  96. data/doc/classes/Bio/DB/SAM/Tools/BamHeaderT.html +0 -169
  97. data/doc/classes/Bio/DB/SAM/Tools/BamHeaderT.src/M000008.html +0 -19
  98. data/doc/classes/Bio/DB/SAM/Tools/BamHeaderT.src/M000009.html +0 -18
  99. data/doc/classes/Bio/DB/SAM/Tools/BamPileup1T.html +0 -111
  100. data/doc/classes/Bio/DB/SAM/Tools/SamfileT.html +0 -129
  101. data/doc/classes/Bio/DB/SAM/Tools/SamfileTX.html +0 -111
  102. data/doc/classes/Bio/DB/SAMException.html +0 -140
  103. data/doc/classes/Bio/DB/SAMException.src/M000016.html +0 -18
  104. data/doc/classes/Bio/DB/Sam.src/M000017.html +0 -43
  105. data/doc/classes/Bio/DB/Sam.src/M000018.html +0 -42
  106. data/doc/classes/Bio/DB/Sam.src/M000019.html +0 -18
  107. data/doc/classes/Bio/DB/Sam.src/M000020.html +0 -22
  108. data/doc/classes/Bio/DB/Sam.src/M000021.html +0 -19
  109. data/doc/classes/Bio/DB/Sam.src/M000022.html +0 -25
  110. data/doc/classes/Bio/DB/Sam.src/M000023.html +0 -28
  111. data/doc/classes/Bio/DB/Sam.src/M000024.html +0 -28
  112. data/doc/classes/Bio/DB/Sam.src/M000025.html +0 -46
  113. data/doc/classes/Bio/DB/Sam.src/M000026.html +0 -24
  114. data/doc/classes/Bio/DB/Sam.src/M000027.html +0 -19
  115. data/doc/classes/Bio/DB/Sam.src/M000028.html +0 -24
  116. data/doc/classes/Bio/DB/Sam.src/M000029.html +0 -41
  117. data/doc/classes/Bio/DB/Sam.src/M000030.html +0 -31
  118. data/doc/classes/Bio/DB/Sam.src/M000031.html +0 -86
  119. data/doc/classes/Bio/DB/Sam.src/M000032.html +0 -34
  120. data/doc/classes/Bio/DB/Tag.html +0 -160
  121. data/doc/classes/Bio/DB/Tag.src/M000011.html +0 -21
  122. data/doc/classes/LibC.html +0 -105
  123. data/doc/classes/Pileup.html +0 -374
  124. data/doc/classes/Pileup.src/M000001.html +0 -34
  125. data/doc/classes/Pileup.src/M000002.html +0 -21
  126. data/doc/classes/Pileup.src/M000003.html +0 -21
  127. data/doc/classes/Pileup.src/M000004.html +0 -21
  128. data/doc/classes/Pileup.src/M000005.html +0 -31
  129. data/doc/files/lib/bio-samtools_rb.html +0 -109
  130. data/doc/files/lib/bio/db/sam/bam_rb.html +0 -108
  131. data/doc/files/lib/bio/db/sam/faidx_rb.html +0 -108
  132. data/doc/files/lib/bio/db/sam/library_rb.html +0 -101
  133. data/doc/files/lib/bio/db/sam/pileup_rb.html +0 -178
  134. data/doc/files/lib/bio/db/sam/sam_rb.html +0 -113
  135. data/doc/files/lib/bio/db/sam_rb.html +0 -111
  136. data/doc/fr_class_index.html +0 -43
  137. data/doc/fr_file_index.html +0 -33
  138. data/doc/fr_method_index.html +0 -58
  139. data/doc/lib/bio-samtools_rb.html +0 -115
  140. data/doc/lib/bio/db/pileup_rb.html +0 -171
  141. data/doc/lib/bio/db/sam/bam_rb.html +0 -121
  142. data/doc/lib/bio/db/sam/faidx_rb.html +0 -117
  143. data/doc/lib/bio/db/sam/library_rb.html +0 -115
  144. data/doc/lib/bio/db/sam/pileup_rb.html +0 -171
  145. data/doc/lib/bio/db/sam/sam_rb.html +0 -121
  146. data/doc/lib/bio/db/sam/vcf_rb.html +0 -124
  147. data/doc/lib/bio/db/sam_rb.html +0 -115
  148. data/doc/lib/bio/db/vcf_rb.html +0 -124
  149. data/doc/rdoc-style.css +0 -208
  150. data/lib/bio/db/sam/bam.rb +0 -210
  151. data/lib/bio/db/sam/sam.rb +0 -86
  152. data/test/samples/pipe_char/test.bam +0 -0
  153. data/test/samples/pipe_char/test.bam.bai +0 -0
  154. data/test/samples/pipe_char/test.tam +0 -10
  155. data/test/samples/pipe_char/test_chr.fasta +0 -1000
  156. data/test/samples/pipe_char/test_chr.fasta.fai +0 -1
  157. data/test/samples/small/test +0 -0
  158. data/test/samples/small/test.bam +0 -0
  159. data/test/samples/small/test.fa +0 -20
  160. data/test/samples/small/test.fai +0 -0
data/doc/classes/Pileup.src/M000001.html DELETED
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- <?xml version="1.0" encoding="iso-8859-1"?>
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- <html>
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- <head>
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- <title>new (Pileup)</title>
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- <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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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/pileup.rb, line 34</span>
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- <span class="ruby-keyword kw">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 re">/\t/</span>)
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- <span class="ruby-keyword kw">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 cmt">##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 kw">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 cmt">##incase anyone tries to use deprecated pileup with -c flag we get upto 13 cols...</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-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-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 kw">else</span>
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- <span class="ruby-comment cmt">#raise RuntimeError, &quot;parsing line '#{pile_up_line.chomp}' failed&quot;</span>
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- <span class="ruby-keyword kw">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 kw">nil</span>
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- <span class="ruby-ivar">@non_ref_count_hash</span> = <span class="ruby-keyword kw">nil</span>
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- <span class="ruby-ivar">@non_ref_count</span> = <span class="ruby-keyword kw">nil</span>
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- <span class="ruby-keyword kw">end</span></pre>
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- </body>
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data/doc/classes/Pileup.src/M000002.html DELETED
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- <head>
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- <title>non_refs (Pileup)</title>
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- <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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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/pileup.rb, line 56</span>
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- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">non_refs</span>
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- <span class="ruby-keyword kw">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-identifier">:A</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">read_bases</span>.<span class="ruby-identifier">count</span>(<span class="ruby-value str">&quot;Aa&quot;</span>), <span class="ruby-identifier">:C</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">read_bases</span>.<span class="ruby-identifier">count</span>(<span class="ruby-value str">&quot;Cc&quot;</span>), <span class="ruby-identifier">:G</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">read_bases</span>.<span class="ruby-identifier">count</span>(<span class="ruby-value str">&quot;Gg&quot;</span>), <span class="ruby-identifier">:T</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">read_bases</span>.<span class="ruby-identifier">count</span>(<span class="ruby-value str">&quot;Tt&quot;</span>)}
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- <span class="ruby-keyword kw">end</span>
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- <span class="ruby-ivar">@non_ref_count_hash</span>
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- <span class="ruby-keyword kw">end</span></pre>
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- <pre><span class="ruby-comment cmt"># File lib/bio/db/sam/pileup.rb, line 64</span>
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- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">non_ref_count</span>
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- <span class="ruby-keyword kw">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-value str">&quot;ATGCatgc&quot;</span>).<span class="ruby-identifier">to_f</span>
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- <span class="ruby-keyword kw">end</span>
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- <span class="ruby-ivar">@non_ref_count</span>
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- <span class="ruby-keyword kw">end</span></pre>
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- <pre><span class="ruby-comment cmt"># File lib/bio/db/sam/pileup.rb, line 72</span>
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- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">ref_count</span>
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- <span class="ruby-keyword kw">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 kw">self</span>.<span class="ruby-identifier">read_bases</span>.<span class="ruby-identifier">count</span>(<span class="ruby-value str">&quot;.,&quot;</span>)
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- <span class="ruby-keyword kw">end</span>
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- <pre><span class="ruby-comment cmt"># File lib/bio/db/sam/pileup.rb, line 80</span>
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- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">consensus</span>
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- <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@consensus</span>.<span class="ruby-identifier">nil?</span>
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- <span class="ruby-identifier">max</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">non_refs</span>.<span class="ruby-identifier">values</span>.<span class="ruby-identifier">max</span>
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- <span class="ruby-keyword kw">if</span> (<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">ref_count</span> <span class="ruby-operator">/</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">coverage</span>) <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span><span class="ruby-value">.5</span>
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- <span class="ruby-ivar">@consensus</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">ref_base</span>
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- <span class="ruby-keyword kw">elsif</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">ref_count</span> <span class="ruby-operator">&gt;</span> <span class="ruby-identifier">max</span>
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- <span class="ruby-ivar">@consensus</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">ref_base</span>
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- <span class="ruby-keyword kw">else</span>
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- <span class="ruby-identifier">arr</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">non_refs</span>.<span class="ruby-identifier">select</span> {<span class="ruby-operator">|</span><span class="ruby-identifier">k</span>,<span class="ruby-identifier">v</span><span class="ruby-operator">|</span> <span class="ruby-identifier">v</span> <span class="ruby-operator">==</span> <span class="ruby-identifier">max</span> }
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- <span class="ruby-identifier">bases</span> = <span class="ruby-identifier">arr</span>.<span class="ruby-identifier">collect</span> {<span class="ruby-operator">|</span><span class="ruby-identifier">b</span><span class="ruby-operator">|</span> <span class="ruby-identifier">b</span>[<span class="ruby-value">0</span>].<span class="ruby-identifier">to_s</span> }
24
- <span class="ruby-identifier">bases</span> <span class="ruby-operator">&lt;&lt;</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">ref_base</span> <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">ref_count</span> <span class="ruby-operator">==</span> <span class="ruby-identifier">max</span>
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- <span class="ruby-ivar">@consensus</span> = <span class="ruby-identifier">bases</span>.<span class="ruby-identifier">sort</span>.<span class="ruby-identifier">join</span>
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- <span class="ruby-keyword kw">end</span>
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- <span class="ruby-keyword kw">end</span>
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- <span class="ruby-ivar">@consensus</span>
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- <span class="ruby-keyword kw">end</span></pre>
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- </tr>
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- <td><strong>Last Update:</strong></td>
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- <td>lib/bio/db/sam/faidx.rb
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- </td>
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- </tr>
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- <tr class="top-aligned-row">
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- <td><strong>Last Update:</strong></td>
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- <td>Wed Oct 26 21:06:33 +0100 2011</td>
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- </tr>
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- </table>
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- </div>
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- <!-- banner header -->
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- <p>
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- require &#8216;rubygems&#8217; require&#8216;ffi&#8217; require
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- &#8216;bio/db/sam/bam&#8216;
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- </p>
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