bio-samtools-wrapper 2.7.0
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- checksums.yaml +7 -0
- data/.document +5 -0
- data/.travis.yml +27 -0
- data/Gemfile +20 -0
- data/LICENSE.txt +702 -0
- data/README.md +501 -0
- data/Rakefile +73 -0
- data/VERSION +1 -0
- data/bin/bam_consensus.rb +85 -0
- data/bio-samtools-wrapper.gemspec +181 -0
- data/doc/Bio/DB/Alignment.html +552 -0
- data/doc/Bio/DB/Pileup.html +711 -0
- data/doc/Bio/DB/SAM/Library.html +167 -0
- data/doc/Bio/DB/SAM/Tools.html +109 -0
- data/doc/Bio/DB/SAM.html +1853 -0
- data/doc/Bio/DB/Tag.html +208 -0
- data/doc/Bio/DB/Vcf.html +431 -0
- data/doc/Bio/DB.html +105 -0
- data/doc/Bio.html +175 -0
- data/doc/LICENSE_txt.html +846 -0
- data/doc/created.rid +9 -0
- data/doc/fonts/Lato-Light.ttf +0 -0
- data/doc/fonts/Lato-LightItalic.ttf +0 -0
- data/doc/fonts/Lato-Regular.ttf +0 -0
- data/doc/fonts/Lato-RegularItalic.ttf +0 -0
- data/doc/fonts/SourceCodePro-Bold.ttf +0 -0
- data/doc/fonts/SourceCodePro-Regular.ttf +0 -0
- data/doc/fonts.css +167 -0
- data/doc/images/add.png +0 -0
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- data/doc/images/wrench_orange.png +0 -0
- data/doc/images/zoom.png +0 -0
- data/doc/index.html +106 -0
- data/doc/js/darkfish.js +140 -0
- data/doc/js/jquery.js +18 -0
- data/doc/js/navigation.js +142 -0
- data/doc/js/search.js +109 -0
- data/doc/js/search_index.js +1 -0
- data/doc/js/searcher.js +228 -0
- data/doc/rdoc.css +580 -0
- data/doc/table_of_contents.html +305 -0
- data/ext/Makefile-bioruby.patch +12 -0
- data/ext/Makefile-suse.patch +11 -0
- data/ext/mkrf_conf.rb +118 -0
- data/lib/bio/BIOExtensions.rb +89 -0
- data/lib/bio/db/alignment.rb +64 -0
- data/lib/bio/db/fastadb.rb +320 -0
- data/lib/bio/db/pileup.rb +273 -0
- data/lib/bio/db/sam/external/COPYING +21 -0
- data/lib/bio/db/sam/external/VERSION +1 -0
- data/lib/bio/db/sam/library.rb +32 -0
- data/lib/bio/db/sam.rb +778 -0
- data/lib/bio/db/vcf.rb +105 -0
- data/lib/bio-samtools-wrapper.rb +9 -0
- data/test/.gitignore +1 -0
- data/test/helper.rb +18 -0
- data/test/sample.vcf +24 -0
- data/test/samples/.gitignore +1 -0
- data/test/samples/LCI/NC_001988.ffn +2 -0
- data/test/samples/LCI/test.bam +0 -0
- data/test/samples/LCI/test.bam.bai +0 -0
- data/test/samples/small/dupes.bam +0 -0
- data/test/samples/small/dupes.sam +274 -0
- data/test/samples/small/ids2.txt +1 -0
- data/test/samples/small/map_for_reheader.sam +8 -0
- data/test/samples/small/map_to_merge1.bam +0 -0
- data/test/samples/small/map_to_merge1.bam.bai +0 -0
- data/test/samples/small/map_to_merge1.sam +8 -0
- data/test/samples/small/map_to_merge2.bam +0 -0
- data/test/samples/small/map_to_merge2.bam.bai +0 -0
- data/test/samples/small/map_to_merge2.sam +8 -0
- data/test/samples/small/no_md.sam +8 -0
- data/test/samples/small/sorted.bam +0 -0
- data/test/samples/small/sorted.bam.bai +0 -0
- data/test/samples/small/test.sai +0 -0
- data/test/samples/small/test.tam +10 -0
- data/test/samples/small/test_chr.fasta +1000 -0
- data/test/samples/small/test_chr.fasta.1.bt2 +0 -0
- data/test/samples/small/test_chr.fasta.2.bt2 +0 -0
- data/test/samples/small/test_chr.fasta.3.bt2 +0 -0
- data/test/samples/small/test_chr.fasta.4.bt2 +0 -0
- data/test/samples/small/test_chr.fasta.amb +2 -0
- data/test/samples/small/test_chr.fasta.ann +3 -0
- data/test/samples/small/test_chr.fasta.bwt +0 -0
- data/test/samples/small/test_chr.fasta.pac +0 -0
- data/test/samples/small/test_chr.fasta.rbwt +0 -0
- data/test/samples/small/test_chr.fasta.rev.1.bt2 +0 -0
- data/test/samples/small/test_chr.fasta.rev.2.bt2 +0 -0
- data/test/samples/small/test_chr.fasta.rpac +0 -0
- data/test/samples/small/test_chr.fasta.rsa +0 -0
- data/test/samples/small/test_chr.fasta.sa +0 -0
- data/test/samples/small/test_cov.svg +273 -0
- data/test/samples/small/test_fastadb.fasta +34 -0
- data/test/samples/small/testu.bam +0 -0
- data/test/samples/small/testu.bed +2 -0
- data/test/test_bio-samtools-wrapper.rb +1 -0
- data/test/test_fastadb.rb +89 -0
- data/test/test_pileup.rb +90 -0
- data/test/test_sam.rb +421 -0
- data/test/test_vcf.rb +79 -0
- data/tutorial/tutorial.html +474 -0
- data/tutorial/tutorial.md +424 -0
- data/tutorial/tutorial.pdf +0 -0
- metadata +254 -0
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}
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main h6 {
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margin: 2em 0 0.5em;
|
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font-size: 1em;
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}
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main p {
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margin: 0 0 0.5em;
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line-height: 1.4em;
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}
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main pre {
|
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margin: 1.2em 0.5em;
|
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padding: 1em;
|
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font-size: 0.8em;
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}
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|
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main hr {
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margin: 1.5em 1em;
|
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border: 2px solid #ddd;
|
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}
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|
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main blockquote {
|
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margin: 0 2em 1.2em 1.2em;
|
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padding-left: 0.5em;
|
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border-left: 2px solid #ddd;
|
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}
|
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|
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main ol,
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main ul {
|
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margin: 1em 2em;
|
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}
|
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|
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main li > p {
|
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margin-bottom: 0.5em;
|
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}
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|
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main dl {
|
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margin: 1em 0.5em;
|
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}
|
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+
|
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|
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main dt {
|
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margin-bottom: 0.5em;
|
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|
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font-weight: bold;
|
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|
+
}
|
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|
+
|
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|
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main dd {
|
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|
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margin: 0 1em 1em 0.5em;
|
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|
+
}
|
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|
+
|
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|
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main header h2 {
|
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|
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margin-top: 2em;
|
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|
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border-width: 0;
|
364
|
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border-top: 4px solid #bbb;
|
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|
+
font-size: 130%;
|
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|
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}
|
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|
+
|
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|
+
main header h3 {
|
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|
+
margin: 2em 0 1.5em;
|
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|
+
border-width: 0;
|
371
|
+
border-top: 3px solid #bbb;
|
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|
+
font-size: 120%;
|
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|
+
}
|
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|
+
|
375
|
+
.documentation-section-title {
|
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|
+
position: relative;
|
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|
+
}
|
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|
+
.documentation-section-title .section-click-top {
|
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|
+
position: absolute;
|
380
|
+
top: 6px;
|
381
|
+
left: 12px;
|
382
|
+
font-size: 10px;
|
383
|
+
color: #9b9877;
|
384
|
+
visibility: hidden;
|
385
|
+
padding-left: 0.5px;
|
386
|
+
}
|
387
|
+
|
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|
+
.documentation-section-title:hover .section-click-top {
|
389
|
+
visibility: visible;
|
390
|
+
}
|
391
|
+
|
392
|
+
.constants-list > dl {
|
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|
+
margin: 1em 0 2em;
|
394
|
+
border: 0;
|
395
|
+
}
|
396
|
+
|
397
|
+
.constants-list > dl dt {
|
398
|
+
margin-bottom: 0.75em;
|
399
|
+
padding-left: 0;
|
400
|
+
font-family: "Source Code Pro", Monaco, monospace;
|
401
|
+
font-size: 110%;
|
402
|
+
}
|
403
|
+
|
404
|
+
.constants-list > dl dt a {
|
405
|
+
color: inherit;
|
406
|
+
}
|
407
|
+
|
408
|
+
.constants-list > dl dd {
|
409
|
+
margin: 0 0 2em 0;
|
410
|
+
padding: 0;
|
411
|
+
color: #666;
|
412
|
+
}
|
413
|
+
|
414
|
+
.documentation-section h2 {
|
415
|
+
position: relative;
|
416
|
+
}
|
417
|
+
|
418
|
+
.documentation-section h2 a {
|
419
|
+
position: absolute;
|
420
|
+
top: 8px;
|
421
|
+
right: 10px;
|
422
|
+
font-size: 12px;
|
423
|
+
color: #9b9877;
|
424
|
+
visibility: hidden;
|
425
|
+
}
|
426
|
+
|
427
|
+
.documentation-section h2:hover a {
|
428
|
+
visibility: visible;
|
429
|
+
}
|
430
|
+
|
431
|
+
/* @group Method Details */
|
432
|
+
|
433
|
+
main .method-source-code {
|
434
|
+
display: none;
|
435
|
+
}
|
436
|
+
|
437
|
+
main .method-description .method-calls-super {
|
438
|
+
color: #333;
|
439
|
+
font-weight: bold;
|
440
|
+
}
|
441
|
+
|
442
|
+
main .method-detail {
|
443
|
+
margin-bottom: 2.5em;
|
444
|
+
cursor: pointer;
|
445
|
+
}
|
446
|
+
|
447
|
+
main .method-detail:target {
|
448
|
+
margin-left: -10px;
|
449
|
+
border-left: 10px solid #f1edba;
|
450
|
+
}
|
451
|
+
|
452
|
+
main .method-heading {
|
453
|
+
position: relative;
|
454
|
+
font-family: "Source Code Pro", Monaco, monospace;
|
455
|
+
font-size: 110%;
|
456
|
+
font-weight: bold;
|
457
|
+
color: #333;
|
458
|
+
}
|
459
|
+
main .method-heading :link,
|
460
|
+
main .method-heading :visited {
|
461
|
+
color: inherit;
|
462
|
+
}
|
463
|
+
main .method-click-advice {
|
464
|
+
position: absolute;
|
465
|
+
top: 2px;
|
466
|
+
right: 5px;
|
467
|
+
font-size: 12px;
|
468
|
+
color: #9b9877;
|
469
|
+
visibility: hidden;
|
470
|
+
padding-right: 20px;
|
471
|
+
line-height: 20px;
|
472
|
+
background: url(images/zoom.png) no-repeat right top;
|
473
|
+
}
|
474
|
+
main .method-heading:hover .method-click-advice {
|
475
|
+
visibility: visible;
|
476
|
+
}
|
477
|
+
|
478
|
+
main .method-alias .method-heading {
|
479
|
+
color: #666;
|
480
|
+
}
|
481
|
+
|
482
|
+
main .method-description,
|
483
|
+
main .aliases {
|
484
|
+
margin-top: 0.75em;
|
485
|
+
color: #333;
|
486
|
+
}
|
487
|
+
|
488
|
+
main .aliases {
|
489
|
+
padding-top: 4px;
|
490
|
+
font-style: italic;
|
491
|
+
cursor: default;
|
492
|
+
}
|
493
|
+
main .method-description ul {
|
494
|
+
margin-left: 1.5em;
|
495
|
+
}
|
496
|
+
|
497
|
+
main #attribute-method-details .method-detail:hover {
|
498
|
+
background-color: transparent;
|
499
|
+
cursor: default;
|
500
|
+
}
|
501
|
+
main .attribute-access-type {
|
502
|
+
text-transform: uppercase;
|
503
|
+
padding: 0 1em;
|
504
|
+
}
|
505
|
+
/* @end */
|
506
|
+
|
507
|
+
/* @end */
|
508
|
+
|
509
|
+
/* @group Source Code */
|
510
|
+
|
511
|
+
pre {
|
512
|
+
margin: 0.5em 0;
|
513
|
+
border: 1px dashed #999;
|
514
|
+
padding: 0.5em;
|
515
|
+
background: #262626;
|
516
|
+
color: white;
|
517
|
+
overflow: auto;
|
518
|
+
}
|
519
|
+
|
520
|
+
.ruby-constant { color: #7fffd4; background: transparent; }
|
521
|
+
.ruby-keyword { color: #00ffff; background: transparent; }
|
522
|
+
.ruby-ivar { color: #eedd82; background: transparent; }
|
523
|
+
.ruby-operator { color: #00ffee; background: transparent; }
|
524
|
+
.ruby-identifier { color: #ffdead; background: transparent; }
|
525
|
+
.ruby-node { color: #ffa07a; background: transparent; }
|
526
|
+
.ruby-comment { color: #dc0000; background: transparent; }
|
527
|
+
.ruby-regexp { color: #ffa07a; background: transparent; }
|
528
|
+
.ruby-value { color: #7fffd4; background: transparent; }
|
529
|
+
|
530
|
+
/* @end */
|
531
|
+
|
532
|
+
|
533
|
+
/* @group search results */
|
534
|
+
#search-results {
|
535
|
+
font-family: Lato, sans-serif;
|
536
|
+
font-weight: 300;
|
537
|
+
}
|
538
|
+
|
539
|
+
#search-results .search-match {
|
540
|
+
font-family: Helvetica, sans-serif;
|
541
|
+
font-weight: normal;
|
542
|
+
}
|
543
|
+
|
544
|
+
#search-results .search-selected {
|
545
|
+
background: #e8e8e8;
|
546
|
+
border-bottom: 1px solid transparent;
|
547
|
+
}
|
548
|
+
|
549
|
+
#search-results li {
|
550
|
+
list-style: none;
|
551
|
+
border-bottom: 1px solid #aaa;
|
552
|
+
margin-bottom: 0.5em;
|
553
|
+
}
|
554
|
+
|
555
|
+
#search-results li:last-child {
|
556
|
+
border-bottom: none;
|
557
|
+
margin-bottom: 0;
|
558
|
+
}
|
559
|
+
|
560
|
+
#search-results li p {
|
561
|
+
padding: 0;
|
562
|
+
margin: 0.5em;
|
563
|
+
}
|
564
|
+
|
565
|
+
#search-results .search-namespace {
|
566
|
+
font-weight: bold;
|
567
|
+
}
|
568
|
+
|
569
|
+
#search-results li em {
|
570
|
+
background: yellow;
|
571
|
+
font-style: normal;
|
572
|
+
}
|
573
|
+
|
574
|
+
#search-results pre {
|
575
|
+
margin: 0.5em;
|
576
|
+
font-family: "Source Code Pro", Monaco, monospace;
|
577
|
+
}
|
578
|
+
|
579
|
+
/* @end */
|
580
|
+
|