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/table_of_contents.html CHANGED
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- <link type="text/css" media="screen" href="./rdoc.css" rel="stylesheet">
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- <script type="text/javascript" charset="utf-8" src="./js/searcher.js"></script>
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- <script type="text/javascript" charset="utf-8" src="./js/darkfish.js"></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/darkfish.js"></script>
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- <body class="indexpage">
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- <h1>Table of Contents - Pileup</h1>
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+ <body id="top" class="table-of-contents">
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+ <main role="main">
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+ <h1 class="class">Table of Contents - Pileup</h1>
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  <a href="Bio.html">Bio</a>
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+ <li><a href="Bio.html#label-Bio%3A%3ADB%3A%3APileup+">Bio::DB::Pileup </a>
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+ <li><a href="Bio.html#label-Vcf+">Vcf </a>
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  </li>
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- <li class="class">
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  <a href="Bio/DB/Alignment.html">Bio::DB::Alignment</a>
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  </li>
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  <a href="Bio/DB/Pileup.html">Bio::DB::Pileup</a>
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  <a href="Bio/DB/SAM/Tools.html">Bio::DB::SAM::Tools</a>
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- <a href="Bio/DB/SAM/Tools/BamPileup1T.html">Bio::DB::SAM::Tools::BamPileup1T</a>
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- <a href="Bio/DB/SAM/Tools/SamfileT.html">Bio::DB::SAM::Tools::SamfileT</a>
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  <a href="Bio/DB/Sam.html">Bio::DB::Sam</a>
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+ <a href="Bio/DB/Sam.html#method-c-docs">::docs</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/SAM/Library.html#method-c-filename">::filename</a>
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+ &mdash;
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+ <span class="container">Bio::DB::SAM::Library</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Pileup.html#method-c-iupac_to_base">::iupac_to_base</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Pileup</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Pileup.html#method-c-new">::new</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Pileup</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Alignment.html#method-c-new">::new</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Alignment</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Vcf.html#method-c-new">::new</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Vcf</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Sam.html#method-c-new">::new</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Sam.html#method-i-average_coverage">#average_coverage</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Sam.html#method-i-calmd">#calmd</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Sam.html#method-i-cat">#cat</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Sam.html#method-i-chromosome_coverage">#chromosome_coverage</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Sam.html#method-i-depth">#depth</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Sam.html#method-i-faidx">#faidx</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Sam.html#method-i-fetch">#fetch</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Sam.html#method-i-fetch_reference">#fetch_reference</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Sam.html#method-i-fetch_with_function">#fetch_with_function</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Sam.html#method-i-fix_mates">#fix_mates</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Sam.html#method-i-fixmate">#fixmate</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Sam.html#method-i-flag_stats">#flag_stats</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Sam.html#method-i-flagstat">#flagstat</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Pileup.html#method-i-genotype_list">#genotype_list</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Pileup</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Sam.html#method-i-idxstats">#idxstats</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Sam.html#method-i-index">#index</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Sam.html#method-i-index_stats">#index_stats</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Vcf.html#method-i-int_or_raw">#int_or_raw</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Vcf</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Sam.html#method-i-merge">#merge</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Sam.html#method-i-mpileup">#mpileup</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Pileup.html#method-i-non_ref_count">#non_ref_count</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Pileup</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Pileup.html#method-i-non_refs">#non_refs</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Pileup</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Sam.html#method-i-open">#open</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Pileup.html#method-i-parse_indel">#parse_indel</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Pileup</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Vcf.html#method-i-parse_line">#parse_line</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Vcf</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Sam.html#method-i-phase">#phase</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Sam.html#method-i-plot_chromosome_coverage">#plot_chromosome_coverage</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Pileup.html#method-i-ref_count">#ref_count</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Pileup</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Sam.html#method-i-reheader">#reheader</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Sam.html#method-i-remove_duplicates">#remove_duplicates</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Sam.html#method-i-rmdup">#rmdup</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Tag.html#method-i-set">#set</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Tag</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Sam.html#method-i-sort">#sort</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Sam.html#method-i-targetcut">#targetcut</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Pileup.html#method-i-to_s">#to_s</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Pileup</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Pileup.html#method-i-to_vcf">#to_vcf</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Pileup</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Sam.html#method-i-tview">#tview</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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+
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+ <li class="method">
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+ <a href="Bio/DB/Sam.html#method-i-view">#view</a>
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+ &mdash;
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+ <span class="container">Bio::DB::Sam</span>
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  </ul>
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+ </main>
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305
 
data/ext/Rakefile ADDED
@@ -0,0 +1,57 @@
1
+ require 'rbconfig'
2
+ require 'open-uri'
3
+ require 'fileutils'
4
+ include FileUtils::Verbose
5
+ require 'rake/clean'
6
+
7
+ URL = "http://sourceforge.net/projects/samtools/files/samtools/0.1.19/samtools-0.1.19.tar.bz2/download"
8
+
9
+ task :download do
10
+ open(URL) do |uri|
11
+ File.open("samtools-0.1.19.tar.bz2",'wb') do |fout|
12
+ fout.write(uri.read)
13
+ end #fout
14
+ end #uri
15
+ end
16
+
17
+ task :compile do
18
+ sh "tar xvfj samtools-0.1.19.tar.bz2"
19
+ cd("samtools-0.1.19") do
20
+ sh "patch < ../Makefile-bioruby.patch"
21
+ # This patch replace CURSES lib with NCURSES which it is the only one available in OpenSUSE
22
+ sh "patch < ../Makefile-suse.patch"
23
+ case Config::CONFIG['host_os']
24
+ when /linux/
25
+ #sh "CFLAGS='-g -Wall -O2 -fPIC' make -e"
26
+ sh "make"
27
+ cp("libbam.a","/Users/ramirezr/Documents/public_code/bioruby-samtools/ext/../lib/bio/db/sam/external")
28
+ #sh "CFLAGS='-g -Wall -O2 -fPIC' make -e libbam.so.1-local"
29
+ sh "make libbam.so.1-local"
30
+ cp("samtools", "/Users/ramirezr/Documents/public_code/bioruby-samtools/ext/../lib/bio/db/sam/external")
31
+ cp("libbam.so.1","/Users/ramirezr/Documents/public_code/bioruby-samtools/ext/../lib/bio/db/sam/external")
32
+ when /darwin/
33
+ sh "make"
34
+ cp("libbam.a","/Users/ramirezr/Documents/public_code/bioruby-samtools/ext/../lib/bio/db/sam/external")
35
+ sh "make libbam.1.dylib-local"
36
+ cp("libbam.1.dylib","/Users/ramirezr/Documents/public_code/bioruby-samtools/ext/../lib/bio/db/sam/external")
37
+ sh "make"
38
+ cp('samtools', "/Users/ramirezr/Documents/public_code/bioruby-samtools/ext/../lib/bio/db/sam/external")
39
+ when /mswin|mingw/ then raise NotImplementedError, "BWA library is not available for Windows platform"
40
+ end #case
41
+ end #cd
42
+ cd("samtools-0.1.19/bcftools") do
43
+ sh "make"
44
+ cp('bcftools', "/Users/ramirezr/Documents/public_code/bioruby-samtools/ext/../lib/bio/db/sam/external")
45
+ end
46
+ end
47
+
48
+ task :clean do
49
+ cd("samtools-0.1.19") do
50
+ sh "make clean"
51
+ end
52
+ rm("samtools-0.1.19.tar.bz2")
53
+ rm_rf("samtools-0.1.19")
54
+ end
55
+
56
+ task :default => [:download, :compile, :clean]
57
+