bio-samtools 0.6.2 → 2.0.3

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  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
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  24. data/doc/images/add.png +0 -0
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  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
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  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
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  88. data/doc/classes/Bio/DB/SAM.html +0 -510
  89. data/doc/classes/Bio/DB/SAM/Library.html +0 -135
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  91. data/doc/classes/Bio/DB/SAM/Tools.html +0 -278
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  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
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  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
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  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
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  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
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  part of the work. For example, Corresponding Source includes interface
@@ -328,7 +294,7 @@ outside their relationship with you.</p>
328
294
  <p>the conditions stated below. Sublicensing is not allowed; section 10 makes
329
295
  it unnecessary.</p>
330
296
 
331
- <pre>3. Protecting Users' Legal Rights From Anti-Circumvention Law.
297
+ <pre>3. Protecting Users&#39; Legal Rights From Anti-Circumvention Law.
332
298
 
333
299
  No covered work shall be deemed part of an effective technological</pre>
334
300
 
@@ -341,13 +307,13 @@ prohibiting or restricting circumvention of such measures.</p>
341
307
  <p>circumvention of technological measures to the extent such circumvention is
342
308
  effected by exercising rights under this License with respect to the
343
309
  covered work, and you disclaim any intention to limit operation or
344
- modification of the work as a means of enforcing, against the works
345
- users, your or third parties legal rights to forbid circumvention of
310
+ modification of the work as a means of enforcing, against the work&#39;s
311
+ users, your or third parties&#39; legal rights to forbid circumvention of
346
312
  technological measures.</p>
347
313
 
348
314
  <pre>4. Conveying Verbatim Copies.
349
315
 
350
- You may convey verbatim copies of the Program's source code as you</pre>
316
+ You may convey verbatim copies of the Program&#39;s source code as you</pre>
351
317
 
352
318
  <p>receive it, in any medium, provided that you conspicuously and
353
319
  appropriately publish on each copy an appropriate copyright notice; keep
@@ -392,11 +358,11 @@ A compilation of a covered work with other separate and independent</pre>
392
358
 
393
359
  <p>works, which are not by their nature extensions of the covered work, and
394
360
  which are not combined with it such as to form a larger program, in or on a
395
- volume of a storage or distribution medium, is called an “aggregate” if
396
- the compilation and its resulting copyright are not used to limit the
397
- access or legal rights of the compilations users beyond what the
398
- individual works permit. Inclusion of a covered work in an aggregate does
399
- not cause this License to apply to the other parts of the aggregate.</p>
361
+ volume of a storage or distribution medium, is called an “aggregate” if the
362
+ compilation and its resulting copyright are not used to limit the access or
363
+ legal rights of the compilation&#39;s users beyond what the individual
364
+ works permit. Inclusion of a covered work in an aggregate does not cause
365
+ this License to apply to the other parts of the aggregate.</p>
400
366
 
401
367
  <pre>6. Conveying Non-Source Forms.
402
368
 
@@ -458,13 +424,13 @@ conveying the object code work.</p>
458
424
  household purposes, or (2) anything designed or sold for incorporation into
459
425
  a dwelling. In determining whether a product is a consumer product,
460
426
  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>
427
+ product received by a particular user, “normally used” refers to a typical
428
+ or common use of that class of product, regardless of the status of the
429
+ particular user or of the way in which the particular user actually uses,
430
+ or expects or is expected to use, the product. A product is a consumer
431
+ product regardless of whether the product has substantial commercial,
432
+ industrial or non-consumer uses, unless such uses represent the only
433
+ significant mode of use of the product.</p>
468
434
 
469
435
  <pre>&quot;Installation Information&quot; for a User Product means any methods,</pre>
470
436
 
@@ -630,7 +596,7 @@ enforcing compliance by third parties with this License.</p>
630
596
  organization, or merging organizations. If propagation of a covered work
631
597
  results from an entity transaction, each party to that transaction who
632
598
  receives a copy of the work also receives whatever licenses to the work the
633
- partys predecessor in interest had or could give under the previous
599
+ party&#39;s predecessor in interest had or could give under the previous
634
600
  paragraph, plus a right to possession of the Corresponding Source of the
635
601
  work from the predecessor in interest, if the predecessor has it or can get
636
602
  it with reasonable efforts.</p>
@@ -649,9 +615,9 @@ Program or any portion of it.</p>
649
615
  A &quot;contributor&quot; is a copyright holder who authorizes use under this</pre>
650
616
 
651
617
  <p>License of the Program or a work on which the Program is based. The work
652
- thus licensed is called the contributors “contributor version”.</p>
618
+ thus licensed is called the contributor&#39;s “contributor version”.</p>
653
619
 
654
- <pre>A contributor's &quot;essential patent claims&quot; are all patent claims</pre>
620
+ <pre>A contributor&#39;s &quot;essential patent claims&quot; are all patent claims</pre>
655
621
 
656
622
  <p>owned or controlled by the contributor, whether already acquired or
657
623
  hereafter acquired, that would be infringed by some manner, permitted by
@@ -663,17 +629,17 @@ consistent with the requirements of this License.</p>
663
629
 
664
630
  <pre>Each contributor grants you a non-exclusive, worldwide, royalty-free</pre>
665
631
 
666
- <p>patent license under the contributors essential patent claims, to make,
667
- use, sell, offer for sale, import and otherwise run, modify and propagate
668
- the contents of its contributor version.</p>
632
+ <p>patent license under the contributor&#39;s essential patent claims, to
633
+ make, use, sell, offer for sale, import and otherwise run, modify and
634
+ propagate the contents of its contributor version.</p>
669
635
 
670
636
  <pre>In the following three paragraphs, a &quot;patent license&quot; is any express</pre>
671
637
 
672
638
  <p>agreement or commitment, however denominated, not to enforce a patent (such
673
639
  as an express permission to practice a patent or covenant not to sue for
674
- patent infringement). To “grant” such a patent license to a party
675
- means to make such an agreement or commitment not to enforce a patent
676
- against the party.</p>
640
+ patent infringement). To “grant” such a patent license to a party means to
641
+ make such an agreement or commitment not to enforce a patent against the
642
+ party.</p>
677
643
 
678
644
  <pre>If you convey a covered work, knowingly relying on a patent license,</pre>
679
645
 
@@ -684,9 +650,9 @@ you must either (1) cause the Corresponding Source to be so available, or
684
650
  (2) arrange to deprive yourself of the benefit of the patent license for
685
651
  this particular work, or (3) arrange, in a manner consistent with the
686
652
  requirements of this License, to extend the patent license to downstream
687
- recipients. “Knowingly relying” means you have actual knowledge that,
688
- but for the patent license, your conveying the covered work in a country,
689
- or your recipients use of the covered work in a country, would infringe
653
+ recipients. “Knowingly relying” means you have actual knowledge that, but
654
+ for the patent license, your conveying the covered work in a country, or
655
+ your recipient&#39;s use of the covered work in a country, would infringe
690
656
  one or more identifiable patents in that country that you have reason to
691
657
  believe are valid.</p>
692
658
 
@@ -719,7 +685,7 @@ arrangement, or that patent license was granted, prior to 28 March 2007.</p>
719
685
  <p>any implied license or other defenses to infringement that may otherwise be
720
686
  available to you under applicable patent law.</p>
721
687
 
722
- <pre>12. No Surrender of Others' Freedom.
688
+ <pre>12. No Surrender of Others&#39; Freedom.
723
689
 
724
690
  If conditions are imposed on you (whether by court order, agreement or</pre>
725
691
 
@@ -764,7 +730,7 @@ Foundation.</p>
764
730
 
765
731
  <pre>If the Program specifies that a proxy can decide which future</pre>
766
732
 
767
- <p>versions of the GNU General Public License can be used, that proxys
733
+ <p>versions of the GNU General Public License can be used, that proxy&#39;s
768
734
  public statement of acceptance of a version permanently authorizes you to
769
735
  choose that version for the Program.</p>
770
736
 
@@ -778,12 +744,12 @@ or copyright holder as a result of your choosing to follow a later version.</p>
778
744
  THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY</pre>
779
745
 
780
746
  <p>APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
781
- HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM “AS IS” WITHOUT
782
- WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT
783
- LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
784
- PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF
785
- THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME
786
- THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.</p>
747
+ HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM “AS IS” WITHOUT WARRANTY
748
+ OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
749
+ THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
750
+ PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
751
+ IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
752
+ ALL NECESSARY SERVICING, REPAIR OR CORRECTION.</p>
787
753
 
788
754
  <pre>16. Limitation of Liability.
789
755
 
@@ -823,7 +789,7 @@ software which everyone can redistribute and change under these terms.</p>
823
789
  the exclusion of warranty; and each file should have at least the
824
790
  “copyright” line and a pointer to where the full notice is found.</p>
825
791
 
826
- <pre>&lt;one line to give the program's name and a brief idea of what it does.&gt;
792
+ <pre>&lt;one line to give the program&#39;s name and a brief idea of what it does.&gt;
827
793
  Copyright (C) &lt;year&gt; &lt;name of author&gt;
828
794
 
829
795
  This program is free software: you can redistribute it and/or modify
@@ -846,20 +812,20 @@ along with this program. If not, see &lt;http://www.gnu.org/licenses/&gt;.</pre
846
812
  <p>notice like this when it starts in an interactive mode:</p>
847
813
 
848
814
  <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'.
815
+ This program comes with ABSOLUTELY NO WARRANTY; for details type `show w&#39;.
850
816
  This is free software, and you are welcome to redistribute it
851
- under certain conditions; type `show c' for details.</pre>
817
+ under certain conditions; type `show c&#39; for details.</pre>
852
818
 
853
- <p>The hypothetical commands `show w and `show c should show the
819
+ <p>The hypothetical commands `show w&#39; and `show c&#39; should show the
854
820
  appropriate parts of the General Public License. Of course, your
855
- programs commands might be different; for a GUI interface, you would use
856
- an “about box”.</p>
821
+ program&#39;s commands might be different; for a GUI interface, you would
822
+ use an “about box”.</p>
857
823
 
858
824
  <pre>You should also get your employer (if you work as a programmer) or school,</pre>
859
825
 
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>
826
+ <p>if any, to sign a “copyright disclaimer” for the program, if necessary. For
827
+ more information on this, and how to apply and follow the GNU GPL, see
828
+ &lt;<a href="http://www.gnu.org/licenses">www.gnu.org/licenses</a>/&gt;.</p>
863
829
 
864
830
  <pre>The GNU General Public License does not permit incorporating your program</pre>
865
831
 
@@ -868,14 +834,13 @@ may consider it more useful to permit linking proprietary applications with
868
834
  the library. If this is what you want to do, use the GNU Lesser General
869
835
  Public License instead of this License. But first, please read &lt;<a
870
836
  href="http://www.gnu.org/philosophy/why-not-lgpl.html">www.gnu.org/philosophy/why-not-lgpl.html</a>&gt;.</p>
871
-
872
- </div>
837
+ </main>
873
838
 
874
839
 
875
840
 
876
- <footer id="validator-badges">
877
- <p><a href="http://validator.w3.org/check/referer">[Validate]</a>
878
- <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 3.12.
879
- <p>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish Rdoc Generator</a> 3.
841
+ <footer id="validator-badges" role="contentinfo">
842
+ <p><a href="http://validator.w3.org/check/referer">Validate</a>
843
+ <p>Generated by <a href="http://rdoc.rubyforge.org">RDoc</a> 4.1.1.
844
+ <p>Based on <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish</a> by <a href="http://deveiate.org">Michael Granger</a>.
880
845
  </footer>
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846
 
@@ -1,10 +1,9 @@
1
- Mon, 26 Nov 2012 21:26:40 +0000
2
- ./LICENSE.txt Wed, 02 Nov 2011 11:50:27 +0000
3
- ./lib/bio/db/sam.rb Mon, 26 Nov 2012 12:30:26 +0000
4
- ./lib/bio/db/sam/bam.rb Thu, 12 Jan 2012 15:31:33 +0000
5
- ./lib/bio/db/vcf.rb Thu, 12 Jan 2012 15:52:37 +0000
6
- ./lib/bio/db/sam/sam.rb Mon, 07 Nov 2011 10:04:59 +0000
7
- ./lib/bio/db/sam/faidx.rb Wed, 02 Nov 2011 11:50:27 +0000
8
- ./lib/bio/db/pileup.rb Mon, 26 Nov 2012 21:21:33 +0000
9
- ./lib/bio-samtools.rb Wed, 02 Nov 2011 16:15:52 +0000
10
- ./lib/bio/db/sam/library.rb Wed, 02 Nov 2011 13:28:41 +0000
1
+ Tue, 18 Mar 2014 16:07:41 +0000
2
+ ./lib/bio/db/alignment.rb Fri, 07 Mar 2014 11:50:30 +0000
3
+ ./lib/bio/db/pileup.rb Fri, 07 Mar 2014 10:51:34 +0000
4
+ ./lib/bio/db/sam/faidx_old.rb Thu, 28 Nov 2013 11:06:34 +0000
5
+ ./lib/bio/db/sam/library.rb Thu, 28 Nov 2013 11:03:39 +0000
6
+ ./lib/bio/db/sam.rb Tue, 18 Mar 2014 16:04:41 +0000
7
+ ./lib/bio/db/vcf.rb Fri, 07 Mar 2014 12:38:34 +0000
8
+ ./lib/bio-samtools.rb Mon, 17 Mar 2014 15:46:18 +0000
9
+ ./LICENSE.txt Thu, 28 Nov 2013 11:03:38 +0000