bio-samtools-wrapper 2.7.0

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 (125) hide show
  1. checksums.yaml +7 -0
  2. data/.document +5 -0
  3. data/.travis.yml +27 -0
  4. data/Gemfile +20 -0
  5. data/LICENSE.txt +702 -0
  6. data/README.md +501 -0
  7. data/Rakefile +73 -0
  8. data/VERSION +1 -0
  9. data/bin/bam_consensus.rb +85 -0
  10. data/bio-samtools-wrapper.gemspec +181 -0
  11. data/doc/Bio/DB/Alignment.html +552 -0
  12. data/doc/Bio/DB/Pileup.html +711 -0
  13. data/doc/Bio/DB/SAM/Library.html +167 -0
  14. data/doc/Bio/DB/SAM/Tools.html +109 -0
  15. data/doc/Bio/DB/SAM.html +1853 -0
  16. data/doc/Bio/DB/Tag.html +208 -0
  17. data/doc/Bio/DB/Vcf.html +431 -0
  18. data/doc/Bio/DB.html +105 -0
  19. data/doc/Bio.html +175 -0
  20. data/doc/LICENSE_txt.html +846 -0
  21. data/doc/created.rid +9 -0
  22. data/doc/fonts/Lato-Light.ttf +0 -0
  23. data/doc/fonts/Lato-LightItalic.ttf +0 -0
  24. data/doc/fonts/Lato-Regular.ttf +0 -0
  25. data/doc/fonts/Lato-RegularItalic.ttf +0 -0
  26. data/doc/fonts/SourceCodePro-Bold.ttf +0 -0
  27. data/doc/fonts/SourceCodePro-Regular.ttf +0 -0
  28. data/doc/fonts.css +167 -0
  29. data/doc/images/add.png +0 -0
  30. data/doc/images/arrow_up.png +0 -0
  31. data/doc/images/brick.png +0 -0
  32. data/doc/images/brick_link.png +0 -0
  33. data/doc/images/bug.png +0 -0
  34. data/doc/images/bullet_black.png +0 -0
  35. data/doc/images/bullet_toggle_minus.png +0 -0
  36. data/doc/images/bullet_toggle_plus.png +0 -0
  37. data/doc/images/date.png +0 -0
  38. data/doc/images/delete.png +0 -0
  39. data/doc/images/find.png +0 -0
  40. data/doc/images/loadingAnimation.gif +0 -0
  41. data/doc/images/macFFBgHack.png +0 -0
  42. data/doc/images/package.png +0 -0
  43. data/doc/images/page_green.png +0 -0
  44. data/doc/images/page_white_text.png +0 -0
  45. data/doc/images/page_white_width.png +0 -0
  46. data/doc/images/plugin.png +0 -0
  47. data/doc/images/ruby.png +0 -0
  48. data/doc/images/tag_blue.png +0 -0
  49. data/doc/images/tag_green.png +0 -0
  50. data/doc/images/transparent.png +0 -0
  51. data/doc/images/wrench.png +0 -0
  52. data/doc/images/wrench_orange.png +0 -0
  53. data/doc/images/zoom.png +0 -0
  54. data/doc/index.html +106 -0
  55. data/doc/js/darkfish.js +140 -0
  56. data/doc/js/jquery.js +18 -0
  57. data/doc/js/navigation.js +142 -0
  58. data/doc/js/search.js +109 -0
  59. data/doc/js/search_index.js +1 -0
  60. data/doc/js/searcher.js +228 -0
  61. data/doc/rdoc.css +580 -0
  62. data/doc/table_of_contents.html +305 -0
  63. data/ext/Makefile-bioruby.patch +12 -0
  64. data/ext/Makefile-suse.patch +11 -0
  65. data/ext/mkrf_conf.rb +118 -0
  66. data/lib/bio/BIOExtensions.rb +89 -0
  67. data/lib/bio/db/alignment.rb +64 -0
  68. data/lib/bio/db/fastadb.rb +320 -0
  69. data/lib/bio/db/pileup.rb +273 -0
  70. data/lib/bio/db/sam/external/COPYING +21 -0
  71. data/lib/bio/db/sam/external/VERSION +1 -0
  72. data/lib/bio/db/sam/library.rb +32 -0
  73. data/lib/bio/db/sam.rb +778 -0
  74. data/lib/bio/db/vcf.rb +105 -0
  75. data/lib/bio-samtools-wrapper.rb +9 -0
  76. data/test/.gitignore +1 -0
  77. data/test/helper.rb +18 -0
  78. data/test/sample.vcf +24 -0
  79. data/test/samples/.gitignore +1 -0
  80. data/test/samples/LCI/NC_001988.ffn +2 -0
  81. data/test/samples/LCI/test.bam +0 -0
  82. data/test/samples/LCI/test.bam.bai +0 -0
  83. data/test/samples/small/dupes.bam +0 -0
  84. data/test/samples/small/dupes.sam +274 -0
  85. data/test/samples/small/ids2.txt +1 -0
  86. data/test/samples/small/map_for_reheader.sam +8 -0
  87. data/test/samples/small/map_to_merge1.bam +0 -0
  88. data/test/samples/small/map_to_merge1.bam.bai +0 -0
  89. data/test/samples/small/map_to_merge1.sam +8 -0
  90. data/test/samples/small/map_to_merge2.bam +0 -0
  91. data/test/samples/small/map_to_merge2.bam.bai +0 -0
  92. data/test/samples/small/map_to_merge2.sam +8 -0
  93. data/test/samples/small/no_md.sam +8 -0
  94. data/test/samples/small/sorted.bam +0 -0
  95. data/test/samples/small/sorted.bam.bai +0 -0
  96. data/test/samples/small/test.sai +0 -0
  97. data/test/samples/small/test.tam +10 -0
  98. data/test/samples/small/test_chr.fasta +1000 -0
  99. data/test/samples/small/test_chr.fasta.1.bt2 +0 -0
  100. data/test/samples/small/test_chr.fasta.2.bt2 +0 -0
  101. data/test/samples/small/test_chr.fasta.3.bt2 +0 -0
  102. data/test/samples/small/test_chr.fasta.4.bt2 +0 -0
  103. data/test/samples/small/test_chr.fasta.amb +2 -0
  104. data/test/samples/small/test_chr.fasta.ann +3 -0
  105. data/test/samples/small/test_chr.fasta.bwt +0 -0
  106. data/test/samples/small/test_chr.fasta.pac +0 -0
  107. data/test/samples/small/test_chr.fasta.rbwt +0 -0
  108. data/test/samples/small/test_chr.fasta.rev.1.bt2 +0 -0
  109. data/test/samples/small/test_chr.fasta.rev.2.bt2 +0 -0
  110. data/test/samples/small/test_chr.fasta.rpac +0 -0
  111. data/test/samples/small/test_chr.fasta.rsa +0 -0
  112. data/test/samples/small/test_chr.fasta.sa +0 -0
  113. data/test/samples/small/test_cov.svg +273 -0
  114. data/test/samples/small/test_fastadb.fasta +34 -0
  115. data/test/samples/small/testu.bam +0 -0
  116. data/test/samples/small/testu.bed +2 -0
  117. data/test/test_bio-samtools-wrapper.rb +1 -0
  118. data/test/test_fastadb.rb +89 -0
  119. data/test/test_pileup.rb +90 -0
  120. data/test/test_sam.rb +421 -0
  121. data/test/test_vcf.rb +79 -0
  122. data/tutorial/tutorial.html +474 -0
  123. data/tutorial/tutorial.md +424 -0
  124. data/tutorial/tutorial.pdf +0 -0
  125. metadata +254 -0
data/doc/Bio/DB.html ADDED
@@ -0,0 +1,105 @@
1
+ <!DOCTYPE html>
2
+
3
+ <html>
4
+ <head>
5
+ <meta charset="UTF-8">
6
+
7
+ <title>class Bio::DB - Pileup</title>
8
+
9
+ <link href="../fonts.css" rel="stylesheet">
10
+ <link href="../rdoc.css" rel="stylesheet">
11
+
12
+ <script type="text/javascript">
13
+ var rdoc_rel_prefix = "../";
14
+ </script>
15
+
16
+ <script src="../js/jquery.js"></script>
17
+ <script src="../js/navigation.js"></script>
18
+ <script src="../js/search_index.js"></script>
19
+ <script src="../js/search.js"></script>
20
+ <script src="../js/searcher.js"></script>
21
+ <script src="../js/darkfish.js"></script>
22
+
23
+
24
+ <body id="top" role="document" class="class">
25
+ <nav role="navigation">
26
+ <div id="project-navigation">
27
+ <div id="home-section" role="region" title="Quick navigation" class="nav-section">
28
+ <h2>
29
+ <a href="../index.html" rel="home">Home</a>
30
+ </h2>
31
+
32
+ <div id="table-of-contents-navigation">
33
+ <a href="../table_of_contents.html#pages">Pages</a>
34
+ <a href="../table_of_contents.html#classes">Classes</a>
35
+ <a href="../table_of_contents.html#methods">Methods</a>
36
+ </div>
37
+ </div>
38
+
39
+ <div id="search-section" role="search" class="project-section initially-hidden">
40
+ <form action="#" method="get" accept-charset="utf-8">
41
+ <div id="search-field-wrapper">
42
+ <input id="search-field" role="combobox" aria-label="Search"
43
+ aria-autocomplete="list" aria-controls="search-results"
44
+ type="text" name="search" placeholder="Search" spellcheck="false"
45
+ title="Type to search, Up and Down to navigate, Enter to load">
46
+ </div>
47
+
48
+ <ul id="search-results" aria-label="Search Results"
49
+ aria-busy="false" aria-expanded="false"
50
+ aria-atomic="false" class="initially-hidden"></ul>
51
+ </form>
52
+ </div>
53
+
54
+ </div>
55
+
56
+
57
+
58
+ <div id="class-metadata">
59
+
60
+ <div id="parent-class-section" class="nav-section">
61
+ <h3>Parent</h3>
62
+
63
+
64
+ <p class="link">Object
65
+
66
+ </div>
67
+
68
+
69
+
70
+
71
+ </div>
72
+ </nav>
73
+
74
+ <main role="main" aria-labelledby="class-Bio::DB">
75
+ <h1 id="class-Bio::DB" class="class">
76
+ class Bio::DB
77
+ </h1>
78
+
79
+ <section class="description">
80
+
81
+ </section>
82
+
83
+
84
+
85
+
86
+ <section id="5Buntitled-5D" class="documentation-section">
87
+
88
+
89
+
90
+
91
+
92
+
93
+
94
+
95
+
96
+ </section>
97
+ </main>
98
+
99
+
100
+ <footer id="validator-badges" role="contentinfo">
101
+ <p><a href="http://validator.w3.org/check/referer">Validate</a>
102
+ <p>Generated by <a href="http://rdoc.rubyforge.org">RDoc</a> 4.1.1.
103
+ <p>Based on <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish</a> by <a href="http://deveiate.org">Michael Granger</a>.
104
+ </footer>
105
+
data/doc/Bio.html ADDED
@@ -0,0 +1,175 @@
1
+ <!DOCTYPE html>
2
+
3
+ <html>
4
+ <head>
5
+ <meta charset="UTF-8">
6
+
7
+ <title>module Bio - Pileup</title>
8
+
9
+ <link href="./fonts.css" rel="stylesheet">
10
+ <link href="./rdoc.css" rel="stylesheet">
11
+
12
+ <script type="text/javascript">
13
+ var rdoc_rel_prefix = "./";
14
+ </script>
15
+
16
+ <script src="./js/jquery.js"></script>
17
+ <script src="./js/navigation.js"></script>
18
+ <script src="./js/search_index.js"></script>
19
+ <script src="./js/search.js"></script>
20
+ <script src="./js/searcher.js"></script>
21
+ <script src="./js/darkfish.js"></script>
22
+
23
+
24
+ <body id="top" role="document" class="module">
25
+ <nav role="navigation">
26
+ <div id="project-navigation">
27
+ <div id="home-section" role="region" title="Quick navigation" class="nav-section">
28
+ <h2>
29
+ <a href="./index.html" rel="home">Home</a>
30
+ </h2>
31
+
32
+ <div id="table-of-contents-navigation">
33
+ <a href="./table_of_contents.html#pages">Pages</a>
34
+ <a href="./table_of_contents.html#classes">Classes</a>
35
+ <a href="./table_of_contents.html#methods">Methods</a>
36
+ </div>
37
+ </div>
38
+
39
+ <div id="search-section" role="search" class="project-section initially-hidden">
40
+ <form action="#" method="get" accept-charset="utf-8">
41
+ <div id="search-field-wrapper">
42
+ <input id="search-field" role="combobox" aria-label="Search"
43
+ aria-autocomplete="list" aria-controls="search-results"
44
+ type="text" name="search" placeholder="Search" spellcheck="false"
45
+ title="Type to search, Up and Down to navigate, Enter to load">
46
+ </div>
47
+
48
+ <ul id="search-results" aria-label="Search Results"
49
+ aria-busy="false" aria-expanded="false"
50
+ aria-atomic="false" class="initially-hidden"></ul>
51
+ </form>
52
+ </div>
53
+
54
+ </div>
55
+
56
+
57
+ <div class="nav-section">
58
+ <h3>Table of Contents</h3>
59
+
60
+ <ul class="link-list" role="directory">
61
+ <li><a href="#module-Bio-label-Bio%3A%3ADB%3A%3APileup+">Bio::DB::Pileup </a>
62
+ <li><a href="#module-Bio-label-Vcf+">Vcf </a>
63
+ </ul>
64
+ </div>
65
+
66
+
67
+ <div id="class-metadata">
68
+
69
+
70
+
71
+
72
+
73
+ </div>
74
+ </nav>
75
+
76
+ <main role="main" aria-labelledby="module-Bio">
77
+ <h1 id="module-Bio" class="module">
78
+ module Bio
79
+ </h1>
80
+
81
+ <section class="description">
82
+
83
+ <h1 id="module-Bio-label-Bio%3A%3ADB%3A%3APileup+"><a href="Bio/DB/Pileup.html">Bio::DB::Pileup</a> <span><a href="#module-Bio-label-Bio%3A%3ADB%3A%3APileup+">&para;</a> <a href="#documentation">&uarr;</a></span></h1>
84
+
85
+ <p>A class representing information in SAMTools pileup format</p>
86
+ <dl class="rdoc-list note-list"><dt>Author
87
+ <dd>
88
+ <p>Dan MacLean (dan.maclean@tsl.ac.uk)</p>
89
+ </dd></dl>
90
+
91
+ <p>Pileup is described at <a
92
+ 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>.
93
+ Briefly (when you invoke pileup with the -c option):</p>
94
+ <ul><li>
95
+ <p>1 reference sequence name</p>
96
+ </li><li>
97
+ <p>2 reference coordinate</p>
98
+ </li><li>
99
+ <p>(3) reference base, or `*&#39; for an indel line</p>
100
+ </li><li>
101
+ <p>(4) genotype where heterozygotes are encoded in the IUB code: M=A/C, R=A/G,
102
+ W=A/T, S=C/G, Y=C/T and K=G/T; indels are indicated by, for example, +A,
103
+ -A or +CC/-C. There is no difference between */+A or +A/*.</p>
104
+ </li><li>
105
+ <p>(5) Phred-scaled likelihood that the genotype is wrong, which is also
106
+ called `consensus quality&#39;.</p>
107
+ </li><li>
108
+ <p>(6) Phred-scaled likelihood that the genotype is identical to the
109
+ reference, which is also called `SNP quality&#39;. Suppose the reference
110
+ base is A and in alignment we see 17 G and 3 A. We will get a low consensus
111
+ quality because it is difficult to distinguish an A/G heterozygote from a
112
+ G/G homozygote. We will get a high SNP quality, though, because the
113
+ evidence of a SNP is very strong.</p>
114
+ </li><li>
115
+ <p>(7) root mean square (RMS) mapping quality</p>
116
+ </li><li>
117
+ <p>8 # reads covering the position</p>
118
+ </li><li>
119
+ <p>9 read bases at a SNP line (check the manual page for more information);
120
+ the 1st indel allele otherwise</p>
121
+ </li><li>
122
+ <p>10 base quality at a SNP line; the 2nd indel allele otherwise</p>
123
+ </li><li>
124
+ <p>(11) indel line only: # reads directly supporting the 1st indel allele</p>
125
+ </li><li>
126
+ <p>(12) indel line only: # reads directly supporting the 2nd indel allele</p>
127
+ </li><li>
128
+ <p>(13) indel line only: # reads supporting a third indel allele</p>
129
+ </li></ul>
130
+
131
+ <p>If pileup is invoked without `-c&#39;, indel lines and columns between 3
132
+ and 7 inclusive will not be outputted.</p>
133
+
134
+ <p>NB mpileup uses the 6 column output format eg
135
+ “seq2t151tGtGt36t0t99t12t.….……At:9&lt;;;7=&lt;&lt;&lt;&lt;&lt;” Pileup
136
+ provides accessors for all columns (6 or 10 column format) and a few other
137
+ useful methods</p>
138
+
139
+ <p>require &#39;rubygems&#39; require&#39;ffi&#39; require
140
+ &#39;bio/db/sam/bam&#39;</p>
141
+
142
+ <h1 id="module-Bio-label-Vcf+">Vcf <span><a href="#module-Bio-label-Vcf+">&para;</a> <a href="#documentation">&uarr;</a></span></h1>
143
+
144
+ <p>A class representing information in Variant Call Format Forked from vcfruby
145
+ at <a
146
+ href="https://github.com/jesserod/vcfruby">github.com/jesserod/vcfruby</a>
147
+ Modified and tests written by Dan MacLean (dan.maclean@tsl.ac.uk) VCF is
148
+ described at <a
149
+ href="http://www.1000genomes.org/node/101">www.1000genomes.org/node/101</a></p>
150
+
151
+ </section>
152
+
153
+
154
+
155
+
156
+ <section id="5Buntitled-5D" class="documentation-section">
157
+
158
+
159
+
160
+
161
+
162
+
163
+
164
+
165
+
166
+ </section>
167
+ </main>
168
+
169
+
170
+ <footer id="validator-badges" role="contentinfo">
171
+ <p><a href="http://validator.w3.org/check/referer">Validate</a>
172
+ <p>Generated by <a href="http://rdoc.rubyforge.org">RDoc</a> 4.1.1.
173
+ <p>Based on <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish</a> by <a href="http://deveiate.org">Michael Granger</a>.
174
+ </footer>
175
+