bio-samtools 0.6.2 → 2.0.3

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
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/fr_class_index.html DELETED
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- <a href="classes/Bio/DB.html">Bio::DB</a><br />
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- <a href="classes/Bio/DB/Alignment.html">Bio::DB::Alignment</a><br />
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- <a href="classes/Bio/DB/SAM/Tools/Bam1CoreT.html">Bio::DB::SAM::Tools::Bam1CoreT</a><br />
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- <a href="classes/Bio/DB/SAM/Tools/Bam1T.html">Bio::DB::SAM::Tools::Bam1T</a><br />
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- <a href="classes/Bio/DB/SAM/Tools/SamfileTX.html">Bio::DB::SAM::Tools::SamfileTX</a><br />
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- <a href="classes/Bio/DB/SAMException.html">Bio::DB::SAMException</a><br />
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- <a href="classes/Bio/DB/Sam.html">Bio::DB::Sam</a><br />
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- <a href="files/lib/bio/db/sam_rb.html">lib/bio/db/sam.rb</a><br />
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- <a href="classes/Bio/DB/Sam.html#M000024">average_coverage (Bio::DB::Sam)</a><br />
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- <a href="classes/Bio/DB/SAM/Tools.html#M000007">bam_sort (Bio::DB::SAM::Tools)</a><br />
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- <a href="classes/Bio/DB/Sam.html#M000025">chromosome_coverage (Bio::DB::Sam)</a><br />
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- <a href="classes/Bio/DB/Sam.html#M000020">close (Bio::DB::Sam)</a><br />
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- <a href="classes/Pileup.html#M000005">consensus (Pileup)</a><br />
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- <a href="classes/Bio/DB/Sam.html#M000032">deprecated_pileup (Bio::DB::Sam)</a><br />
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- <a href="classes/Bio/DB/Sam.html#M000028">fetch (Bio::DB::Sam)</a><br />
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- <a href="classes/Bio/DB/Sam.html#M000026">fetch_reference (Bio::DB::Sam)</a><br />
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- <a href="classes/Bio/DB/Sam.html#M000029">fetch_with_function (Bio::DB::Sam)</a><br />
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- <a href="classes/Bio/DB/SAM/Library.html#M000006">filename (Bio::DB::SAM::Library)</a><br />
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- <a href="classes/Bio/DB/Alignment.html#M000013">finalize (Bio::DB::Alignment)</a><br />
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- <a href="classes/Bio/DB/Sam.html#M000021">finalize (Bio::DB::Sam)</a><br />
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- <a href="classes/Bio/DB/Sam.html#M000022">load_index (Bio::DB::Sam)</a><br />
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- <a href="classes/Bio/DB/Sam.html#M000023">load_reference (Bio::DB::Sam)</a><br />
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- <a href="classes/Bio/DB/Sam.html#M000030">merge (Bio::DB::Sam)</a><br />
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- <a href="classes/Bio/DB/Sam.html#M000031">mpileup (Bio::DB::Sam)</a><br />
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- <a href="classes/Pileup.html#M000001">new (Pileup)</a><br />
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- <a href="classes/Pileup.html#M000003">non_ref_count (Pileup)</a><br />
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- <a href="classes/Pileup.html#M000002">non_refs (Pileup)</a><br />
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- <a href="classes/Bio/DB/Sam.html#M000018">open (Bio::DB::Sam)</a><br />
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- <a href="classes/Bio/DB/SAM/Tools/Bam1T.html#M000010">qname (Bio::DB::SAM::Tools::Bam1T)</a><br />
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- <a href="classes/Pileup.html#M000004">ref_count (Pileup)</a><br />
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- <a href="classes/Bio/DB/SAM/Tools/BamHeaderT.html#M000009">text (Bio::DB::SAM::Tools::BamHeaderT)</a><br />
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- <a href="classes/Bio/DB/Sam.html#M000019">to_s (Bio::DB::Sam)</a><br />
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- <h1 id="label-Bio%3A%3ADB%3A%3APileup+"><a href="../../../Bio/DB/Pileup.html">Bio::DB::Pileup</a> </h1>
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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>Pileup is described at <a
115
- 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
133
- is A and in alignment we see 17 G and 3 A. We will get a low consensus
134
- quality because it is difficult to distinguish an A/G heterozygote from a
135
- G/G homozygote. We will get a high SNP quality, though, because the
136
- 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>
148
- </li><li>
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- <p>(12) indel line only: # reads directly supporting the 2nd indel allele</p>
150
- </li><li>
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- <p>(13) indel line only: # reads supporting a third indel allele</p>
152
- </li></ul>
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-
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- <p>If pileup is invoked without `-c’, indel lines and columns between 3 and
155
- 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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- Pileup provides accessors for all columns (6 or 10 column format) and a few
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- other useful methods</p>
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- <p>require ‘rubygems’ require ‘ffi’</p>
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- <pre class="ruby"><span class="ruby-identifier">require</span> <span class="ruby-string">'bio/db/sam/faidx'</span>
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