bio-samtools 0.4.1 → 0.4.2

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  1. data/VERSION +1 -1
  2. data/bio-samtools.gemspec +60 -6
  3. data/doc/Bio.html +171 -0
  4. data/doc/Bio/DB.html +163 -0
  5. data/doc/Bio/DB/Alignment.html +780 -0
  6. data/doc/Bio/DB/SAM.html +1241 -0
  7. data/doc/Bio/DB/SAM/Library.html +217 -0
  8. data/doc/Bio/DB/SAM/Tools.html +331 -0
  9. data/doc/Bio/DB/SAM/Tools/Bam1CoreT.html +159 -0
  10. data/doc/Bio/DB/SAM/Tools/Bam1T.html +220 -0
  11. data/doc/Bio/DB/SAM/Tools/BamHeaderT.html +249 -0
  12. data/doc/Bio/DB/SAM/Tools/BamPileup1T.html +159 -0
  13. data/doc/Bio/DB/SAM/Tools/SamfileT.html +171 -0
  14. data/doc/Bio/DB/SAM/Tools/SamfileTX.html +159 -0
  15. data/doc/Bio/DB/SAMException.html +205 -0
  16. data/doc/Bio/DB/Tag.html +254 -0
  17. data/doc/LICENSE_txt.html +881 -0
  18. data/doc/LibC.html +153 -0
  19. data/doc/Pileup.html +571 -0
  20. data/doc/Vcf.html +473 -0
  21. data/doc/created.rid +10 -1
  22. data/doc/images/add.png +0 -0
  23. data/doc/images/brick.png +0 -0
  24. data/doc/images/brick_link.png +0 -0
  25. data/doc/images/bug.png +0 -0
  26. data/doc/images/bullet_black.png +0 -0
  27. data/doc/images/bullet_toggle_minus.png +0 -0
  28. data/doc/images/bullet_toggle_plus.png +0 -0
  29. data/doc/images/date.png +0 -0
  30. data/doc/images/delete.png +0 -0
  31. data/doc/images/find.png +0 -0
  32. data/doc/images/loadingAnimation.gif +0 -0
  33. data/doc/images/macFFBgHack.png +0 -0
  34. data/doc/images/package.png +0 -0
  35. data/doc/images/page_green.png +0 -0
  36. data/doc/images/page_white_text.png +0 -0
  37. data/doc/images/page_white_width.png +0 -0
  38. data/doc/images/plugin.png +0 -0
  39. data/doc/images/ruby.png +0 -0
  40. data/doc/images/tag_blue.png +0 -0
  41. data/doc/images/tag_green.png +0 -0
  42. data/doc/images/transparent.png +0 -0
  43. data/doc/images/wrench.png +0 -0
  44. data/doc/images/wrench_orange.png +0 -0
  45. data/doc/images/zoom.png +0 -0
  46. data/doc/index.html +109 -21
  47. data/doc/js/darkfish.js +153 -0
  48. data/doc/js/jquery.js +18 -0
  49. data/doc/js/navigation.js +142 -0
  50. data/doc/js/search.js +94 -0
  51. data/doc/js/search_index.js +1 -0
  52. data/doc/js/searcher.js +228 -0
  53. data/doc/lib/bio-samtools_rb.html +115 -0
  54. data/doc/lib/bio/db/sam/bam_rb.html +121 -0
  55. data/doc/lib/bio/db/sam/faidx_rb.html +117 -0
  56. data/doc/lib/bio/db/sam/library_rb.html +115 -0
  57. data/doc/lib/bio/db/sam/pileup_rb.html +171 -0
  58. data/doc/lib/bio/db/sam/sam_rb.html +121 -0
  59. data/doc/lib/bio/db/sam/vcf_rb.html +124 -0
  60. data/doc/lib/bio/db/sam_rb.html +115 -0
  61. data/doc/rdoc.css +543 -0
  62. data/doc/table_of_contents.html +186 -0
  63. data/ext/Makefile-bioruby.patch +1 -1
  64. data/ext/Rakefile +8 -1
  65. data/ext/mkrf_conf.rb +8 -1
  66. data/lib/bio/db/sam.rb +140 -27
  67. data/lib/bio/db/sam/vcf.rb +0 -1
  68. data/test/basictest.rb +4 -4
  69. data/test/test_basic.rb +50 -34
  70. metadata +79 -25
  71. data/test/coverage.rb +0 -26
  72. data/test/coverage_plot.rb +0 -28
  73. data/test/feature.rb +0 -0
  74. data/test/test_pileup.rb +0 -68
data/doc/lib/bio/db/sam/vcf_rb.html ADDED
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+ <li><a href="../../../../Bio.html">Bio</a>
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+ <li><a href="../../../../Bio/DB.html">Bio::DB</a>
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+ <li><a href="../../../../Bio/DB/Alignment.html">Bio::DB::Alignment</a>
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+ <li><a href="../../../../Bio/DB/SAM.html">Bio::DB::SAM</a>
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+ <li><a href="../../../../Bio/DB/SAM/Library.html">Bio::DB::SAM::Library</a>
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+ <li><a href="../../../../Bio/DB/SAM/Tools.html">Bio::DB::SAM::Tools</a>
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+ <li><a href="../../../../Bio/DB/SAM/Tools/Bam1CoreT.html">Bio::DB::SAM::Tools::Bam1CoreT</a>
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+
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+ <li><a href="../../../../Bio/DB/SAM/Tools/Bam1T.html">Bio::DB::SAM::Tools::Bam1T</a>
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+
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+ <li><a href="../../../../Bio/DB/SAM/Tools/BamHeaderT.html">Bio::DB::SAM::Tools::BamHeaderT</a>
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+
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+ <li><a href="../../../../Bio/DB/SAM/Tools/BamPileup1T.html">Bio::DB::SAM::Tools::BamPileup1T</a>
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+
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+ <li><a href="../../../../Bio/DB/SAM/Tools/SamfileT.html">Bio::DB::SAM::Tools::SamfileT</a>
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+
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+ <li><a href="../../../../Bio/DB/SAM/Tools/SamfileTX.html">Bio::DB::SAM::Tools::SamfileTX</a>
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+
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+ <li><a href="../../../../Bio/DB/SAMException.html">Bio::DB::SAMException</a>
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+ <li><a href="../../../../Bio/DB/Sam.html">Bio::DB::Sam</a>
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+ <li><a href="../../../../Bio/DB/Tag.html">Bio::DB::Tag</a>
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+ <li><a href="../../../../LibC.html">LibC</a>
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+ <li><a href="../../../../Pileup.html">Pileup</a>
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+ </nav>
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+ <div id="documentation" class="description">
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+
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+ <h1 id="label-Vcf+"><a href="../../../../Vcf.html">Vcf</a> </h1>
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+
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+ <p>A class representing information in Variant Call Format Forked from vcfruby
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+ at <a
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+ href="https://github.com/jesserod/vcfruby">github.com/jesserod/vcfruby</a>
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+ Modified and tests written by Dan MacLean (tsl at dan.maclean.ac.uk) VCF is
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+ href="http://www.1000genomes.org/node/101">www.1000genomes.org/node/101</a></p>
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data/doc/lib/bio/db/sam_rb.html ADDED
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+ <li><a href="../../../Bio.html">Bio</a>
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+ <li><a href="../../../Bio/DB.html">Bio::DB</a>
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+ <li><a href="../../../Bio/DB/Alignment.html">Bio::DB::Alignment</a>
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+ <li><a href="../../../Bio/DB/SAM.html">Bio::DB::SAM</a>
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+ <li><a href="../../../Bio/DB/SAM/Library.html">Bio::DB::SAM::Library</a>
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+ <li><a href="../../../Bio/DB/SAM/Tools.html">Bio::DB::SAM::Tools</a>
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+ <li><a href="../../../Bio/DB/SAM/Tools/SamfileT.html">Bio::DB::SAM::Tools::SamfileT</a>
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+ <li><a href="../../../Bio/DB/SAM/Tools/SamfileTX.html">Bio::DB::SAM::Tools::SamfileTX</a>
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+ }
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+ #project-metadata h3.section-header {
233
+ border-bottom: 1px solid #aaa;
234
+ position: relative;
235
+ }
236
+
237
+ #project-metadata form {
238
+ color: #777;
239
+ background: #ccc;
240
+ }
241
+
242
+ /* @end */
243
+
244
+ /* @group Documentation Section */
245
+ .description {
246
+ font-size: 100%;
247
+ color: #333;
248
+ }
249
+
250
+ .description p {
251
+ margin: 1em 0.4em;
252
+ }
253
+
254
+ .description li p {
255
+ margin: 0;
256
+ }
257
+
258
+ .description ol,
259
+ .description ul {
260
+ margin-left: 1.5em;
261
+ }
262
+ .description ol li,
263
+ .description ul li {
264
+ line-height: 1.4em;
265
+ }
266
+
267
+ .note-list {
268
+ margin: 8px 0;
269
+ }
270
+
271
+ .label-list {
272
+ margin: 8px 1.5em;
273
+ border: 1px solid #ccc;
274
+ }
275
+ .description .label-list {
276
+ font-size: 14px;
277
+ }
278
+
279
+ .note-list dt {
280
+ font-weight: bold;
281
+ }
282
+ .note-list dd {
283
+ padding: 0 12px;
284
+ }
285
+
286
+ .label-list dt {
287
+ padding: 2px 4px;
288
+ font-weight: bold;
289
+ background: #ddd;
290
+ }
291
+ .label-list dd {
292
+ padding: 2px 12px;
293
+ }
294
+ .label-list dd + dt,
295
+ .note-list dd + dt {
296
+ margin-top: 0.7em;
297
+ }
298
+
299
+ #documentation .section {
300
+ font-size: 90%;
301
+ }
302
+
303
+ #documentation h2.section-header {
304
+ margin-top: 1em;
305
+ padding: 0.25em 0.5em;
306
+ background: #ccc;
307
+ color: #333;
308
+ font-size: 175%;
309
+ border: 1px solid #bbb;
310
+ -moz-border-radius: 3px;
311
+ -webkit-border-radius: 3px;
312
+ }
313
+
314
+ .documentation-section-title {
315
+ position: relative;
316
+ }
317
+ .documentation-section-title .section-click-top {
318
+ position: absolute;
319
+ top: 6px;
320
+ right: 12px;
321
+ font-size: 10px;
322
+ color: #9b9877;
323
+ visibility: hidden;
324
+ padding-right: 0.5px;
325
+ }
326
+
327
+ .documentation-section-title:hover .section-click-top {
328
+ visibility: visible;
329
+ }
330
+
331
+ #documentation h3.section-header {
332
+ margin-top: 1em;
333
+ padding: 0.25em 0.5em;
334
+ background-color: #dedede;
335
+ color: #333;
336
+ font-size: 150%;
337
+ border: 1px solid #bbb;
338
+ -moz-border-radius: 3px;
339
+ -webkit-border-radius: 3px;
340
+ }
341
+
342
+ #constants-list > dl,
343
+ #attributes-list > dl {
344
+ margin: 1em 0 2em;
345
+ border: 0;
346
+ }
347
+ #constants-list > dl dt,
348
+ #attributes-list > dl dt {
349
+ padding-left: 0;
350
+ font-weight: bold;
351
+ font-family: Monaco, "Andale Mono";
352
+ background: inherit;
353
+ }
354
+ #constants-list > dl dt a,
355
+ #attributes-list > dl dt a {
356
+ color: inherit;
357
+ }
358
+ #constants-list > dl dd,
359
+ #attributes-list > dl dd {
360
+ margin: 0 0 1em 0;
361
+ padding: 0;
362
+ color: #666;
363
+ }
364
+
365
+ .documentation-section h2 {
366
+ position: relative;
367
+ }
368
+
369
+ .documentation-section h2 a {
370
+ position: absolute;
371
+ top: 8px;
372
+ right: 10px;
373
+ font-size: 12px;
374
+ color: #9b9877;
375
+ visibility: hidden;
376
+ }
377
+
378
+ .documentation-section h2:hover a {
379
+ visibility: visible;
380
+ }
381
+
382
+ /* @group Method Details */
383
+
384
+ #documentation .method-source-code {
385
+ display: none;
386
+ }
387
+
388
+ #documentation .method-detail {
389
+ margin: 0.5em 0;
390
+ padding: 0.5em 0;
391
+ cursor: pointer;
392
+ }
393
+ #documentation .method-detail:hover {
394
+ background-color: #f1edba;
395
+ }
396
+ #documentation .method-heading {
397
+ position: relative;
398
+ padding: 2px 4px 0 20px;
399
+ font-size: 125%;
400
+ font-weight: bold;
401
+ color: #333;
402
+ background: url(images/brick.png) no-repeat left bottom;
403
+ }
404
+ #documentation .method-heading :link,
405
+ #documentation .method-heading :visited {
406
+ color: inherit;
407
+ }
408
+ #documentation .method-click-advice {
409
+ position: absolute;
410
+ top: 2px;
411
+ right: 5px;
412
+ font-size: 10px;
413
+ color: #9b9877;
414
+ visibility: hidden;
415
+ padding-right: 20px;
416
+ line-height: 20px;
417
+ background: url(images/zoom.png) no-repeat right top;
418
+ }
419
+ #documentation .method-heading:hover .method-click-advice {
420
+ visibility: visible;
421
+ }
422
+
423
+ #documentation .method-alias .method-heading {
424
+ color: #666;
425
+ background: url(images/brick_link.png) no-repeat left bottom;
426
+ }
427
+
428
+ #documentation .method-description,
429
+ #documentation .aliases {
430
+ margin: 0 20px;
431
+ color: #666;
432
+ }
433
+
434
+ #documentation .method-description p,
435
+ #documentation .aliases p {
436
+ line-height: 1.2em;
437
+ }
438
+
439
+ #documentation .aliases {
440
+ padding-top: 4px;
441
+ font-style: italic;
442
+ cursor: default;
443
+ }
444
+ #documentation .method-description p {
445
+ margin-bottom: 0.5em;
446
+ }
447
+ #documentation .method-description ul {
448
+ margin-left: 1.5em;
449
+ }
450
+ pre {
451
+ margin: 0.5em 0;
452
+ }
453
+
454
+ #documentation .attribute-method-heading {
455
+ background: url(images/tag_green.png) no-repeat left bottom;
456
+ }
457
+ #documentation #attribute-method-details .method-detail:hover {
458
+ background-color: transparent;
459
+ cursor: default;
460
+ }
461
+ #documentation .attribute-access-type {
462
+ font-size: 60%;
463
+ text-transform: uppercase;
464
+ vertical-align: super;
465
+ padding: 0 2px;
466
+ }
467
+ /* @end */
468
+
469
+ /* @end */
470
+
471
+ /* @group Source Code */
472
+
473
+ pre {
474
+ overflow: auto;
475
+ background: #262626;
476
+ color: white;
477
+ border: 1px dashed #999;
478
+ padding: 0.5em;
479
+ }
480
+
481
+ .description pre {
482
+ margin: 0 0.4em;
483
+ }
484
+
485
+ .ruby-constant { color: #7fffd4; background: transparent; }
486
+ .ruby-keyword { color: #00ffff; background: transparent; }
487
+ .ruby-ivar { color: #eedd82; background: transparent; }
488
+ .ruby-operator { color: #00ffee; background: transparent; }
489
+ .ruby-identifier { color: #ffdead; background: transparent; }
490
+ .ruby-node { color: #ffa07a; background: transparent; }
491
+ .ruby-comment { color: #dc0000; font-weight: bold; background: transparent; }
492
+ .ruby-regexp { color: #ffa07a; background: transparent; }
493
+ .ruby-value { color: #7fffd4; background: transparent; }
494
+
495
+ /* @end */
496
+
497
+
498
+ /* @group search results */
499
+ #search-results h1 {
500
+ font-size: 1em;
501
+ font-weight: normal;
502
+ text-shadow: none;
503
+ }
504
+
505
+ #search-results .current {
506
+ background: #ccc;
507
+ border-bottom: 1px solid transparent;
508
+ }
509
+
510
+ #search-results li {
511
+ list-style: none;
512
+ border-bottom: 1px solid #aaa;
513
+ -moz-border-radius: 4px;
514
+ -webkit-border-radius: 4px;
515
+ border-radius: 4px;
516
+ margin-bottom: 0.5em;
517
+ }
518
+
519
+ #search-results li:last-child {
520
+ border-bottom: none;
521
+ margin-bottom: 0;
522
+ }
523
+
524
+ #search-results li p {
525
+ padding: 0;
526
+ margin: 0.5em;
527
+ }
528
+
529
+ #search-results .search-namespace {
530
+ font-weight: bold;
531
+ }
532
+
533
+ #search-results li em {
534
+ background: yellow;
535
+ font-style: normal;
536
+ }
537
+
538
+ #search-results pre {
539
+ margin: 0.5em;
540
+ }
541
+
542
+ /* @end */
543
+