bio-samtools 0.4.1 → 0.4.2

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Files changed (74) hide show
  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
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  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/LICENSE_txt.html ADDED
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+ <p>of sections 4 and 5, provided that you also convey the machine-readable
406
+ Corresponding Source under the terms of this License, in one of these ways:</p>
407
+
408
+ <pre class="ruby"> <span class="ruby-identifier">a</span>) <span class="ruby-constant">Convey</span> <span class="ruby-identifier">the</span> <span class="ruby-identifier">object</span> <span class="ruby-identifier">code</span> <span class="ruby-keyword">in</span>, <span class="ruby-keyword">or</span> <span class="ruby-identifier">embodied</span> <span class="ruby-keyword">in</span>, <span class="ruby-identifier">a</span> <span class="ruby-identifier">physical</span> <span class="ruby-identifier">product</span>
409
+ (<span class="ruby-identifier">including</span> <span class="ruby-identifier">a</span> <span class="ruby-identifier">physical</span> <span class="ruby-identifier">distribution</span> <span class="ruby-identifier">medium</span>), <span class="ruby-identifier">accompanied</span> <span class="ruby-identifier">by</span> <span class="ruby-identifier">the</span>
410
+ <span class="ruby-constant">Corresponding</span> <span class="ruby-constant">Source</span> <span class="ruby-identifier">fixed</span> <span class="ruby-identifier">on</span> <span class="ruby-identifier">a</span> <span class="ruby-identifier">durable</span> <span class="ruby-identifier">physical</span> <span class="ruby-identifier">medium</span>
411
+ <span class="ruby-identifier">customarily</span> <span class="ruby-identifier">used</span> <span class="ruby-keyword">for</span> <span class="ruby-identifier">software</span> <span class="ruby-identifier">interchange</span>.
412
+
413
+ <span class="ruby-identifier">b</span>) <span class="ruby-constant">Convey</span> <span class="ruby-identifier">the</span> <span class="ruby-identifier">object</span> <span class="ruby-identifier">code</span> <span class="ruby-keyword">in</span>, <span class="ruby-keyword">or</span> <span class="ruby-identifier">embodied</span> <span class="ruby-keyword">in</span>, <span class="ruby-identifier">a</span> <span class="ruby-identifier">physical</span> <span class="ruby-identifier">product</span>
414
+ (<span class="ruby-identifier">including</span> <span class="ruby-identifier">a</span> <span class="ruby-identifier">physical</span> <span class="ruby-identifier">distribution</span> <span class="ruby-identifier">medium</span>), <span class="ruby-identifier">accompanied</span> <span class="ruby-identifier">by</span> <span class="ruby-identifier">a</span>
415
+ <span class="ruby-identifier">written</span> <span class="ruby-identifier">offer</span>, <span class="ruby-identifier">valid</span> <span class="ruby-keyword">for</span> <span class="ruby-identifier">at</span> <span class="ruby-identifier">least</span> <span class="ruby-identifier">three</span> <span class="ruby-identifier">years</span> <span class="ruby-keyword">and</span> <span class="ruby-identifier">valid</span> <span class="ruby-keyword">for</span> <span class="ruby-identifier">as</span>
416
+ <span class="ruby-identifier">long</span> <span class="ruby-identifier">as</span> <span class="ruby-identifier">you</span> <span class="ruby-identifier">offer</span> <span class="ruby-identifier">spare</span> <span class="ruby-identifier">parts</span> <span class="ruby-keyword">or</span> <span class="ruby-identifier">customer</span> <span class="ruby-identifier">support</span> <span class="ruby-keyword">for</span> <span class="ruby-identifier">that</span> <span class="ruby-identifier">product</span>
417
+ <span class="ruby-identifier">model</span>, <span class="ruby-identifier">to</span> <span class="ruby-identifier">give</span> <span class="ruby-identifier">anyone</span> <span class="ruby-identifier">who</span> <span class="ruby-identifier">possesses</span> <span class="ruby-identifier">the</span> <span class="ruby-identifier">object</span> <span class="ruby-identifier">code</span> <span class="ruby-identifier">either</span> (<span class="ruby-value">1</span>) <span class="ruby-identifier">a</span>
418
+ <span class="ruby-identifier">copy</span> <span class="ruby-identifier">of</span> <span class="ruby-identifier">the</span> <span class="ruby-constant">Corresponding</span> <span class="ruby-constant">Source</span> <span class="ruby-keyword">for</span> <span class="ruby-identifier">all</span> <span class="ruby-identifier">the</span> <span class="ruby-identifier">software</span> <span class="ruby-keyword">in</span> <span class="ruby-identifier">the</span>
419
+ <span class="ruby-identifier">product</span> <span class="ruby-identifier">that</span> <span class="ruby-identifier">is</span> <span class="ruby-identifier">covered</span> <span class="ruby-identifier">by</span> <span class="ruby-identifier">this</span> <span class="ruby-constant">License</span>, <span class="ruby-identifier">on</span> <span class="ruby-identifier">a</span> <span class="ruby-identifier">durable</span> <span class="ruby-identifier">physical</span>
420
+ <span class="ruby-identifier">medium</span> <span class="ruby-identifier">customarily</span> <span class="ruby-identifier">used</span> <span class="ruby-keyword">for</span> <span class="ruby-identifier">software</span> <span class="ruby-identifier">interchange</span>, <span class="ruby-keyword">for</span> <span class="ruby-identifier">a</span> <span class="ruby-identifier">price</span> <span class="ruby-identifier">no</span>
421
+ <span class="ruby-identifier">more</span> <span class="ruby-identifier">than</span> <span class="ruby-identifier">your</span> <span class="ruby-identifier">reasonable</span> <span class="ruby-identifier">cost</span> <span class="ruby-identifier">of</span> <span class="ruby-identifier">physically</span> <span class="ruby-identifier">performing</span> <span class="ruby-identifier">this</span>
422
+ <span class="ruby-identifier">conveying</span> <span class="ruby-identifier">of</span> <span class="ruby-identifier">source</span>, <span class="ruby-keyword">or</span> (<span class="ruby-value">2</span>) <span class="ruby-identifier">access</span> <span class="ruby-identifier">to</span> <span class="ruby-identifier">copy</span> <span class="ruby-identifier">the</span>
423
+ <span class="ruby-constant">Corresponding</span> <span class="ruby-constant">Source</span> <span class="ruby-identifier">from</span> <span class="ruby-identifier">a</span> <span class="ruby-identifier">network</span> <span class="ruby-identifier">server</span> <span class="ruby-identifier">at</span> <span class="ruby-identifier">no</span> <span class="ruby-identifier">charge</span>.
424
+
425
+ <span class="ruby-identifier">c</span>) <span class="ruby-constant">Convey</span> <span class="ruby-identifier">individual</span> <span class="ruby-identifier">copies</span> <span class="ruby-identifier">of</span> <span class="ruby-identifier">the</span> <span class="ruby-identifier">object</span> <span class="ruby-identifier">code</span> <span class="ruby-identifier">with</span> <span class="ruby-identifier">a</span> <span class="ruby-identifier">copy</span> <span class="ruby-identifier">of</span> <span class="ruby-identifier">the</span>
426
+ <span class="ruby-identifier">written</span> <span class="ruby-identifier">offer</span> <span class="ruby-identifier">to</span> <span class="ruby-identifier">provide</span> <span class="ruby-identifier">the</span> <span class="ruby-constant">Corresponding</span> <span class="ruby-constant">Source</span>. <span class="ruby-constant">This</span>
427
+ <span class="ruby-identifier">alternative</span> <span class="ruby-identifier">is</span> <span class="ruby-identifier">allowed</span> <span class="ruby-identifier">only</span> <span class="ruby-identifier">occasionally</span> <span class="ruby-keyword">and</span> <span class="ruby-identifier">noncommercially</span>, <span class="ruby-keyword">and</span>
428
+ <span class="ruby-identifier">only</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">you</span> <span class="ruby-identifier">received</span> <span class="ruby-identifier">the</span> <span class="ruby-identifier">object</span> <span class="ruby-identifier">code</span> <span class="ruby-identifier">with</span> <span class="ruby-identifier">such</span> <span class="ruby-identifier">an</span> <span class="ruby-identifier">offer</span>, <span class="ruby-keyword">in</span> <span class="ruby-identifier">accord</span>
429
+ <span class="ruby-identifier">with</span> <span class="ruby-identifier">subsection</span> <span class="ruby-value">6</span><span class="ruby-identifier">b</span>.
430
+
431
+ <span class="ruby-identifier">d</span>) <span class="ruby-constant">Convey</span> <span class="ruby-identifier">the</span> <span class="ruby-identifier">object</span> <span class="ruby-identifier">code</span> <span class="ruby-identifier">by</span> <span class="ruby-identifier">offering</span> <span class="ruby-identifier">access</span> <span class="ruby-identifier">from</span> <span class="ruby-identifier">a</span> <span class="ruby-identifier">designated</span>
432
+ <span class="ruby-identifier">place</span> (<span class="ruby-identifier">gratis</span> <span class="ruby-keyword">or</span> <span class="ruby-keyword">for</span> <span class="ruby-identifier">a</span> <span class="ruby-identifier">charge</span>), <span class="ruby-keyword">and</span> <span class="ruby-identifier">offer</span> <span class="ruby-identifier">equivalent</span> <span class="ruby-identifier">access</span> <span class="ruby-identifier">to</span> <span class="ruby-identifier">the</span>
433
+ <span class="ruby-constant">Corresponding</span> <span class="ruby-constant">Source</span> <span class="ruby-keyword">in</span> <span class="ruby-identifier">the</span> <span class="ruby-identifier">same</span> <span class="ruby-identifier">way</span> <span class="ruby-identifier">through</span> <span class="ruby-identifier">the</span> <span class="ruby-identifier">same</span> <span class="ruby-identifier">place</span> <span class="ruby-identifier">at</span> <span class="ruby-identifier">no</span>
434
+ <span class="ruby-identifier">further</span> <span class="ruby-identifier">charge</span>. <span class="ruby-constant">You</span> <span class="ruby-identifier">need</span> <span class="ruby-keyword">not</span> <span class="ruby-identifier">require</span> <span class="ruby-identifier">recipients</span> <span class="ruby-identifier">to</span> <span class="ruby-identifier">copy</span> <span class="ruby-identifier">the</span>
435
+ <span class="ruby-constant">Corresponding</span> <span class="ruby-constant">Source</span> <span class="ruby-identifier">along</span> <span class="ruby-identifier">with</span> <span class="ruby-identifier">the</span> <span class="ruby-identifier">object</span> <span class="ruby-identifier">code</span>. <span class="ruby-constant">If</span> <span class="ruby-identifier">the</span> <span class="ruby-identifier">place</span> <span class="ruby-identifier">to</span>
436
+ <span class="ruby-identifier">copy</span> <span class="ruby-identifier">the</span> <span class="ruby-identifier">object</span> <span class="ruby-identifier">code</span> <span class="ruby-identifier">is</span> <span class="ruby-identifier">a</span> <span class="ruby-identifier">network</span> <span class="ruby-identifier">server</span>, <span class="ruby-identifier">the</span> <span class="ruby-constant">Corresponding</span> <span class="ruby-constant">Source</span>
437
+ <span class="ruby-identifier">may</span> <span class="ruby-identifier">be</span> <span class="ruby-identifier">on</span> <span class="ruby-identifier">a</span> <span class="ruby-identifier">different</span> <span class="ruby-identifier">server</span> (<span class="ruby-identifier">operated</span> <span class="ruby-identifier">by</span> <span class="ruby-identifier">you</span> <span class="ruby-keyword">or</span> <span class="ruby-identifier">a</span> <span class="ruby-identifier">third</span> <span class="ruby-identifier">party</span>)
438
+ <span class="ruby-identifier">that</span> <span class="ruby-identifier">supports</span> <span class="ruby-identifier">equivalent</span> <span class="ruby-identifier">copying</span> <span class="ruby-identifier">facilities</span>, <span class="ruby-identifier">provided</span> <span class="ruby-identifier">you</span> <span class="ruby-identifier">maintain</span>
439
+ <span class="ruby-identifier">clear</span> <span class="ruby-identifier">directions</span> <span class="ruby-keyword">next</span> <span class="ruby-identifier">to</span> <span class="ruby-identifier">the</span> <span class="ruby-identifier">object</span> <span class="ruby-identifier">code</span> <span class="ruby-identifier">saying</span> <span class="ruby-identifier">where</span> <span class="ruby-identifier">to</span> <span class="ruby-identifier">find</span> <span class="ruby-identifier">the</span>
440
+ <span class="ruby-constant">Corresponding</span> <span class="ruby-constant">Source</span>. <span class="ruby-constant">Regardless</span> <span class="ruby-identifier">of</span> <span class="ruby-identifier">what</span> <span class="ruby-identifier">server</span> <span class="ruby-identifier">hosts</span> <span class="ruby-identifier">the</span>
441
+ <span class="ruby-constant">Corresponding</span> <span class="ruby-constant">Source</span>, <span class="ruby-identifier">you</span> <span class="ruby-identifier">remain</span> <span class="ruby-identifier">obligated</span> <span class="ruby-identifier">to</span> <span class="ruby-keyword">ensure</span> <span class="ruby-identifier">that</span> <span class="ruby-identifier">it</span> <span class="ruby-identifier">is</span>
442
+ <span class="ruby-identifier">available</span> <span class="ruby-keyword">for</span> <span class="ruby-identifier">as</span> <span class="ruby-identifier">long</span> <span class="ruby-identifier">as</span> <span class="ruby-identifier">needed</span> <span class="ruby-identifier">to</span> <span class="ruby-identifier">satisfy</span> <span class="ruby-identifier">these</span> <span class="ruby-identifier">requirements</span>.
443
+
444
+ <span class="ruby-identifier">e</span>) <span class="ruby-constant">Convey</span> <span class="ruby-identifier">the</span> <span class="ruby-identifier">object</span> <span class="ruby-identifier">code</span> <span class="ruby-identifier">using</span> <span class="ruby-identifier">peer</span><span class="ruby-operator">-</span><span class="ruby-identifier">to</span><span class="ruby-operator">-</span><span class="ruby-identifier">peer</span> <span class="ruby-identifier">transmission</span>, <span class="ruby-identifier">provided</span>
445
+ <span class="ruby-identifier">you</span> <span class="ruby-identifier">inform</span> <span class="ruby-identifier">other</span> <span class="ruby-identifier">peers</span> <span class="ruby-identifier">where</span> <span class="ruby-identifier">the</span> <span class="ruby-identifier">object</span> <span class="ruby-identifier">code</span> <span class="ruby-keyword">and</span> <span class="ruby-constant">Corresponding</span>
446
+ <span class="ruby-constant">Source</span> <span class="ruby-identifier">of</span> <span class="ruby-identifier">the</span> <span class="ruby-identifier">work</span> <span class="ruby-identifier">are</span> <span class="ruby-identifier">being</span> <span class="ruby-identifier">offered</span> <span class="ruby-identifier">to</span> <span class="ruby-identifier">the</span> <span class="ruby-identifier">general</span> <span class="ruby-identifier">public</span> <span class="ruby-identifier">at</span> <span class="ruby-identifier">no</span>
447
+ <span class="ruby-identifier">charge</span> <span class="ruby-identifier">under</span> <span class="ruby-identifier">subsection</span> <span class="ruby-value">6</span><span class="ruby-identifier">d</span>.
448
+
449
+ <span class="ruby-constant">A</span> <span class="ruby-identifier">separable</span> <span class="ruby-identifier">portion</span> <span class="ruby-identifier">of</span> <span class="ruby-identifier">the</span> <span class="ruby-identifier">object</span> <span class="ruby-identifier">code</span>, <span class="ruby-identifier">whose</span> <span class="ruby-identifier">source</span> <span class="ruby-identifier">code</span> <span class="ruby-identifier">is</span> <span class="ruby-identifier">excluded</span>
450
+ </pre>
451
+
452
+ <p>from the Corresponding Source as a System Library, need not be included in
453
+ conveying the object code work.</p>
454
+
455
+ <pre>A &quot;User Product&quot; is either (1) a &quot;consumer product&quot;, which means any</pre>
456
+
457
+ <p>tangible personal property which is normally used for personal, family, or
458
+ household purposes, or (2) anything designed or sold for incorporation into
459
+ a dwelling. In determining whether a product is a consumer product,
460
+ doubtful cases shall be resolved in favor of coverage. For a particular
461
+ product received by a particular user, “normally used” refers to a
462
+ typical or common use of that class of product, regardless of the status of
463
+ the particular user or of the way in which the particular user actually
464
+ uses, or expects or is expected to use, the product. A product is a
465
+ consumer product regardless of whether the product has substantial
466
+ commercial, industrial or non-consumer uses, unless such uses represent the
467
+ only significant mode of use of the product.</p>
468
+
469
+ <pre>&quot;Installation Information&quot; for a User Product means any methods,</pre>
470
+
471
+ <p>procedures, authorization keys, or other information required to install
472
+ and execute modified versions of a covered work in that User Product from a
473
+ modified version of its Corresponding Source. The information must suffice
474
+ to ensure that the continued functioning of the modified object code is in
475
+ no case prevented or interfered with solely because modification has been
476
+ made.</p>
477
+
478
+ <pre>If you convey an object code work under this section in, or with, or</pre>
479
+
480
+ <p>specifically for use in, a User Product, and the conveying occurs as part
481
+ of a transaction in which the right of possession and use of the User
482
+ Product is transferred to the recipient in perpetuity or for a fixed term
483
+ (regardless of how the transaction is characterized), the Corresponding
484
+ Source conveyed under this section must be accompanied by the Installation
485
+ Information. But this requirement does not apply if neither you nor any
486
+ third party retains the ability to install modified object code on the User
487
+ Product (for example, the work has been installed in ROM).</p>
488
+
489
+ <pre>The requirement to provide Installation Information does not include a</pre>
490
+
491
+ <p>requirement to continue to provide support service, warranty, or updates
492
+ for a work that has been modified or installed by the recipient, or for the
493
+ User Product in which it has been modified or installed. Access to a
494
+ network may be denied when the modification itself materially and adversely
495
+ affects the operation of the network or violates the rules and protocols
496
+ for communication across the network.</p>
497
+
498
+ <pre>Corresponding Source conveyed, and Installation Information provided,</pre>
499
+
500
+ <p>in accord with this section must be in a format that is publicly documented
501
+ (and with an implementation available to the public in source code form),
502
+ and must require no special password or key for unpacking, reading or
503
+ copying.</p>
504
+
505
+ <pre>7. Additional Terms.
506
+
507
+ &quot;Additional permissions&quot; are terms that supplement the terms of this</pre>
508
+
509
+ <p>License by making exceptions from one or more of its conditions. Additional
510
+ permissions that are applicable to the entire Program shall be treated as
511
+ though they were included in this License, to the extent that they are
512
+ valid under applicable law. If additional permissions apply only to part
513
+ of the Program, that part may be used separately under those permissions,
514
+ but the entire Program remains governed by this License without regard to
515
+ the additional permissions.</p>
516
+
517
+ <pre>When you convey a copy of a covered work, you may at your option</pre>
518
+
519
+ <p>remove any additional permissions from that copy, or from any part of it.
520
+ (Additional permissions may be written to require their own removal in
521
+ certain cases when you modify the work.) You may place additional
522
+ permissions on material, added by you to a covered work, for which you have
523
+ or can give appropriate copyright permission.</p>
524
+
525
+ <pre>Notwithstanding any other provision of this License, for material you</pre>
526
+
527
+ <p>add to a covered work, you may (if authorized by the copyright holders of
528
+ that material) supplement the terms of this License with terms:</p>
529
+
530
+ <pre> a) Disclaiming warranty or limiting liability differently from the
531
+ terms of sections 15 and 16 of this License; or
532
+
533
+ b) Requiring preservation of specified reasonable legal notices or
534
+ author attributions in that material or in the Appropriate Legal
535
+ Notices displayed by works containing it; or
536
+
537
+ c) Prohibiting misrepresentation of the origin of that material, or
538
+ requiring that modified versions of such material be marked in
539
+ reasonable ways as different from the original version; or
540
+
541
+ d) Limiting the use for publicity purposes of names of licensors or
542
+ authors of the material; or
543
+
544
+ e) Declining to grant rights under trademark law for use of some
545
+ trade names, trademarks, or service marks; or
546
+
547
+ f) Requiring indemnification of licensors and authors of that
548
+ material by anyone who conveys the material (or modified versions of
549
+ it) with contractual assumptions of liability to the recipient, for
550
+ any liability that these contractual assumptions directly impose on
551
+ those licensors and authors.
552
+
553
+ All other non-permissive additional terms are considered &quot;further</pre>
554
+
555
+ <p>restrictions“ within the meaning of section 10. If the Program as you
556
+ received it, or any part of it, contains a notice stating that it is
557
+ governed by this License along with a term that is a further restriction,
558
+ you may remove that term. If a license document contains a further
559
+ restriction but permits relicensing or conveying under this License, you
560
+ may add to a covered work material governed by the terms of that license
561
+ document, provided that the further restriction does not survive such
562
+ relicensing or conveying.</p>
563
+
564
+ <pre>If you add terms to a covered work in accord with this section, you</pre>
565
+
566
+ <p>must place, in the relevant source files, a statement of the additional
567
+ terms that apply to those files, or a notice indicating where to find the
568
+ applicable terms.</p>
569
+
570
+ <pre>Additional terms, permissive or non-permissive, may be stated in the</pre>
571
+
572
+ <p>form of a separately written license, or stated as exceptions; the above
573
+ requirements apply either way.</p>
574
+
575
+ <pre>8. Termination.
576
+
577
+ You may not propagate or modify a covered work except as expressly</pre>
578
+
579
+ <p>provided under this License. Any attempt otherwise to propagate or modify
580
+ it is void, and will automatically terminate your rights under this License
581
+ (including any patent licenses granted under the third paragraph of section
582
+ 11).</p>
583
+
584
+ <pre>However, if you cease all violation of this License, then your</pre>
585
+
586
+ <p>license from a particular copyright holder is reinstated (a) provisionally,
587
+ unless and until the copyright holder explicitly and finally terminates
588
+ your license, and (b) permanently, if the copyright holder fails to notify
589
+ you of the violation by some reasonable means prior to 60 days after the
590
+ cessation.</p>
591
+
592
+ <pre>Moreover, your license from a particular copyright holder is</pre>
593
+
594
+ <p>reinstated permanently if the copyright holder notifies you of the
595
+ violation by some reasonable means, this is the first time you have
596
+ received notice of violation of this License (for any work) from that
597
+ copyright holder, and you cure the violation prior to 30 days after your
598
+ receipt of the notice.</p>
599
+
600
+ <pre>Termination of your rights under this section does not terminate the</pre>
601
+
602
+ <p>licenses of parties who have received copies or rights from you under this
603
+ License. If your rights have been terminated and not permanently
604
+ reinstated, you do not qualify to receive new licenses for the same
605
+ material under section 10.</p>
606
+
607
+ <pre>9. Acceptance Not Required for Having Copies.
608
+
609
+ You are not required to accept this License in order to receive or</pre>
610
+
611
+ <p>run a copy of the Program. Ancillary propagation of a covered work
612
+ occurring solely as a consequence of using peer-to-peer transmission to
613
+ receive a copy likewise does not require acceptance. However, nothing
614
+ other than this License grants you permission to propagate or modify any
615
+ covered work. These actions infringe copyright if you do not accept this
616
+ License. Therefore, by modifying or propagating a covered work, you
617
+ indicate your acceptance of this License to do so.</p>
618
+
619
+ <pre>10. Automatic Licensing of Downstream Recipients.
620
+
621
+ Each time you convey a covered work, the recipient automatically</pre>
622
+
623
+ <p>receives a license from the original licensors, to run, modify and
624
+ propagate that work, subject to this License. You are not responsible for
625
+ enforcing compliance by third parties with this License.</p>
626
+
627
+ <pre>An &quot;entity transaction&quot; is a transaction transferring control of an</pre>
628
+
629
+ <p>organization, or substantially all assets of one, or subdividing an
630
+ organization, or merging organizations. If propagation of a covered work
631
+ results from an entity transaction, each party to that transaction who
632
+ receives a copy of the work also receives whatever licenses to the work the
633
+ party’s predecessor in interest had or could give under the previous
634
+ paragraph, plus a right to possession of the Corresponding Source of the
635
+ work from the predecessor in interest, if the predecessor has it or can get
636
+ it with reasonable efforts.</p>
637
+
638
+ <pre>You may not impose any further restrictions on the exercise of the</pre>
639
+
640
+ <p>rights granted or affirmed under this License. For example, you may not
641
+ impose a license fee, royalty, or other charge for exercise of rights
642
+ granted under this License, and you may not initiate litigation (including
643
+ a cross-claim or counterclaim in a lawsuit) alleging that any patent claim
644
+ is infringed by making, using, selling, offering for sale, or importing the
645
+ Program or any portion of it.</p>
646
+
647
+ <pre>11. Patents.
648
+
649
+ A &quot;contributor&quot; is a copyright holder who authorizes use under this</pre>
650
+
651
+ <p>License of the Program or a work on which the Program is based. The work
652
+ thus licensed is called the contributor’s “contributor version”.</p>
653
+
654
+ <pre>A contributor's &quot;essential patent claims&quot; are all patent claims</pre>
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+
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+ <p>owned or controlled by the contributor, whether already acquired or
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+ hereafter acquired, that would be infringed by some manner, permitted by
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+ this License, of making, using, or selling its contributor version, but do
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+ not include claims that would be infringed only as a consequence of further
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+ modification of the contributor version. For purposes of this definition,
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+ “control” includes the right to grant patent sublicenses in a manner
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+ consistent with the requirements of this License.</p>
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+
664
+ <pre>Each contributor grants you a non-exclusive, worldwide, royalty-free</pre>
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+ <p>patent license under the contributor’s essential patent claims, to make,
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+ use, sell, offer for sale, import and otherwise run, modify and propagate
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+ the contents of its contributor version.</p>
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+
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+ <pre>In the following three paragraphs, a &quot;patent license&quot; is any express</pre>
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672
+ <p>agreement or commitment, however denominated, not to enforce a patent (such
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+ as an express permission to practice a patent or covenant not to sue for
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+ patent infringement). To “grant” such a patent license to a party
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+ means to make such an agreement or commitment not to enforce a patent
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+ against the party.</p>
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+
678
+ <pre>If you convey a covered work, knowingly relying on a patent license,</pre>
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+ <p>and the Corresponding Source of the work is not available for anyone to
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+ copy, free of charge and under the terms of this License, through a
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+ publicly available network server or other readily accessible means, then
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+ you must either (1) cause the Corresponding Source to be so available, or
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+ (2) arrange to deprive yourself of the benefit of the patent license for
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+ this particular work, or (3) arrange, in a manner consistent with the
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+ requirements of this License, to extend the patent license to downstream
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+ recipients. “Knowingly relying” means you have actual knowledge that,
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+ but for the patent license, your conveying the covered work in a country,
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+ or your recipient’s use of the covered work in a country, would infringe
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+ one or more identifiable patents in that country that you have reason to
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+ believe are valid.</p>
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+
693
+ <pre>If, pursuant to or in connection with a single transaction or</pre>
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+
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+ <p>arrangement, you convey, or propagate by procuring conveyance of, a covered
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+ work, and grant a patent license to some of the parties receiving the
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+ covered work authorizing them to use, propagate, modify or convey a
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+ specific copy of the covered work, then the patent license you grant is
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+ automatically extended to all recipients of the covered work and works
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+ based on it.</p>
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+
702
+ <pre>A patent license is &quot;discriminatory&quot; if it does not include within</pre>
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+
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+ <p>the scope of its coverage, prohibits the exercise of, or is conditioned on
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+ the non-exercise of one or more of the rights that are specifically granted
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+ under this License. You may not convey a covered work if you are a party
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+ to an arrangement with a third party that is in the business of
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+ distributing software, under which you make payment to the third party
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+ based on the extent of your activity of conveying the work, and under which
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+ the third party grants, to any of the parties who would receive the covered
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+ work from you, a discriminatory patent license (a) in connection with
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+ copies of the covered work conveyed by you (or copies made from those
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+ copies), or (b) primarily for and in connection with specific products or
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+ compilations that contain the covered work, unless you entered into that
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+ arrangement, or that patent license was granted, prior to 28 March 2007.</p>
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+
717
+ <pre>Nothing in this License shall be construed as excluding or limiting</pre>
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+
719
+ <p>any implied license or other defenses to infringement that may otherwise be
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+ available to you under applicable patent law.</p>
721
+
722
+ <pre>12. No Surrender of Others' Freedom.
723
+
724
+ If conditions are imposed on you (whether by court order, agreement or</pre>
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+
726
+ <p>otherwise) that contradict the conditions of this License, they do not
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+ excuse you from the conditions of this License. If you cannot convey a
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+ covered work so as to satisfy simultaneously your obligations under this
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+ License and any other pertinent obligations, then as a consequence you may
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+ not convey it at all. For example, if you agree to terms that obligate you
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+ to collect a royalty for further conveying from those to whom you convey
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+ the Program, the only way you could satisfy both those terms and this
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+ License would be to refrain entirely from conveying the Program.</p>
734
+
735
+ <pre>13. Use with the GNU Affero General Public License.
736
+
737
+ Notwithstanding any other provision of this License, you have</pre>
738
+
739
+ <p>permission to link or combine any covered work with a work licensed under
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+ version 3 of the GNU Affero General Public License into a single combined
741
+ work, and to convey the resulting work. The terms of this License will
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+ continue to apply to the part which is the covered work, but the special
743
+ requirements of the GNU Affero General Public License, section 13,
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+ concerning interaction through a network will apply to the combination as
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+ such.</p>
746
+
747
+ <pre>14. Revised Versions of this License.
748
+
749
+ The Free Software Foundation may publish revised and/or new versions of</pre>
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+
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+ <p>the GNU General Public License from time to time. Such new versions will
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+ be similar in spirit to the present version, but may differ in detail to
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+ address new problems or concerns.</p>
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+
755
+ <pre>Each version is given a distinguishing version number. If the</pre>
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+
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+ <p>Program specifies that a certain numbered version of the GNU General Public
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+ License “or any later version” applies to it, you have the option of
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+ following the terms and conditions either of that numbered version or of
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+ any later version published by the Free Software Foundation. If the
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+ Program does not specify a version number of the GNU General Public
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+ License, you may choose any version ever published by the Free Software
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+ Foundation.</p>
764
+
765
+ <pre>If the Program specifies that a proxy can decide which future</pre>
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+
767
+ <p>versions of the GNU General Public License can be used, that proxy’s
768
+ public statement of acceptance of a version permanently authorizes you to
769
+ choose that version for the Program.</p>
770
+
771
+ <pre>Later license versions may give you additional or different</pre>
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+
773
+ <p>permissions. However, no additional obligations are imposed on any author
774
+ or copyright holder as a result of your choosing to follow a later version.</p>
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+
776
+ <pre>15. Disclaimer of Warranty.
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+
778
+ THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY</pre>
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+
780
+ <p>APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
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+ HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM “AS IS” WITHOUT
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+ WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT
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+ LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
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+ PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF
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+ THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME
786
+ THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.</p>
787
+
788
+ <pre>16. Limitation of Liability.
789
+
790
+ IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING</pre>
791
+
792
+ <p>WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
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+ THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
794
+ GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
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+ USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
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+ DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
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+ PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
798
+ EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
799
+ SUCH DAMAGES.</p>
800
+
801
+ <pre>17. Interpretation of Sections 15 and 16.
802
+
803
+ If the disclaimer of warranty and limitation of liability provided</pre>
804
+
805
+ <p>above cannot be given local legal effect according to their terms,
806
+ reviewing courts shall apply local law that most closely approximates an
807
+ absolute waiver of all civil liability in connection with the Program,
808
+ unless a warranty or assumption of liability accompanies a copy of the
809
+ Program in return for a fee.</p>
810
+
811
+ <pre> END OF TERMS AND CONDITIONS
812
+
813
+ How to Apply These Terms to Your New Programs
814
+
815
+ If you develop a new program, and you want it to be of the greatest</pre>
816
+
817
+ <p>possible use to the public, the best way to achieve this is to make it free
818
+ software which everyone can redistribute and change under these terms.</p>
819
+
820
+ <pre>To do so, attach the following notices to the program. It is safest</pre>
821
+
822
+ <p>to attach them to the start of each source file to most effectively state
823
+ the exclusion of warranty; and each file should have at least the
824
+ “copyright” line and a pointer to where the full notice is found.</p>
825
+
826
+ <pre>&lt;one line to give the program's name and a brief idea of what it does.&gt;
827
+ Copyright (C) &lt;year&gt; &lt;name of author&gt;
828
+
829
+ This program is free software: you can redistribute it and/or modify
830
+ it under the terms of the GNU General Public License as published by
831
+ the Free Software Foundation, either version 3 of the License, or
832
+ (at your option) any later version.
833
+
834
+ This program is distributed in the hope that it will be useful,
835
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
836
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
837
+ GNU General Public License for more details.
838
+
839
+ You should have received a copy of the GNU General Public License
840
+ along with this program. If not, see &lt;http://www.gnu.org/licenses/&gt;.</pre>
841
+
842
+ <p>Also add information on how to contact you by electronic and paper mail.</p>
843
+
844
+ <pre>If the program does terminal interaction, make it output a short</pre>
845
+
846
+ <p>notice like this when it starts in an interactive mode:</p>
847
+
848
+ <pre>&lt;program&gt; Copyright (C) &lt;year&gt; &lt;name of author&gt;
849
+ This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
850
+ This is free software, and you are welcome to redistribute it
851
+ under certain conditions; type `show c' for details.</pre>
852
+
853
+ <p>The hypothetical commands `show w’ and `show c’ should show the
854
+ appropriate parts of the General Public License. Of course, your
855
+ program’s commands might be different; for a GUI interface, you would use
856
+ an “about box”.</p>
857
+
858
+ <pre>You should also get your employer (if you work as a programmer) or school,</pre>
859
+
860
+ <p>if any, to sign a “copyright disclaimer” for the program, if necessary.
861
+ For more information on this, and how to apply and follow the GNU GPL, see
862
+ &lt;<a href="http://www.gnu.org/licenses/">www.gnu.org/licenses/</a>&gt;.</p>
863
+
864
+ <pre>The GNU General Public License does not permit incorporating your program</pre>
865
+
866
+ <p>into proprietary programs. If your program is a subroutine library, you
867
+ may consider it more useful to permit linking proprietary applications with
868
+ the library. If this is what you want to do, use the GNU Lesser General
869
+ Public License instead of this License. But first, please read &lt;<a
870
+ href="http://www.gnu.org/philosophy/why-not-lgpl.html">www.gnu.org/philosophy/why-not-lgpl.html</a>&gt;.</p>
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