bio-samtools 0.2.5 → 0.3.0

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Files changed (73) hide show
  1. data/README.rdoc +7 -20
  2. data/Rakefile +11 -0
  3. data/VERSION +1 -1
  4. data/bio-samtools.gemspec +67 -1
  5. data/doc/basic_styles.css +31 -0
  6. data/doc/classes/Bio.html +139 -0
  7. data/doc/classes/Bio/DB.html +137 -0
  8. data/doc/classes/Bio/DB/Alignment.html +441 -0
  9. data/doc/classes/Bio/DB/Alignment.src/M000012.html +19 -0
  10. data/doc/classes/Bio/DB/Alignment.src/M000013.html +27 -0
  11. data/doc/classes/Bio/DB/Alignment.src/M000014.html +45 -0
  12. data/doc/classes/Bio/DB/Alignment.src/M000015.html +40 -0
  13. data/doc/classes/Bio/DB/SAM.html +510 -0
  14. data/doc/classes/Bio/DB/SAM/Library.html +135 -0
  15. data/doc/classes/Bio/DB/SAM/Library.src/M000006.html +28 -0
  16. data/doc/classes/Bio/DB/SAM/Tools.html +278 -0
  17. data/doc/classes/Bio/DB/SAM/Tools.src/M000007.html +20 -0
  18. data/doc/classes/Bio/DB/SAM/Tools/Bam1CoreT.html +111 -0
  19. data/doc/classes/Bio/DB/SAM/Tools/Bam1T.html +150 -0
  20. data/doc/classes/Bio/DB/SAM/Tools/Bam1T.src/M000010.html +20 -0
  21. data/doc/classes/Bio/DB/SAM/Tools/BamHeaderT.html +169 -0
  22. data/doc/classes/Bio/DB/SAM/Tools/BamHeaderT.src/M000008.html +19 -0
  23. data/doc/classes/Bio/DB/SAM/Tools/BamHeaderT.src/M000009.html +18 -0
  24. data/doc/classes/Bio/DB/SAM/Tools/BamPileup1T.html +111 -0
  25. data/doc/classes/Bio/DB/SAM/Tools/SamfileT.html +129 -0
  26. data/doc/classes/Bio/DB/SAM/Tools/SamfileTX.html +111 -0
  27. data/doc/classes/Bio/DB/SAMException.html +140 -0
  28. data/doc/classes/Bio/DB/SAMException.src/M000016.html +18 -0
  29. data/doc/classes/Bio/DB/Sam.src/M000017.html +43 -0
  30. data/doc/classes/Bio/DB/Sam.src/M000018.html +42 -0
  31. data/doc/classes/Bio/DB/Sam.src/M000019.html +18 -0
  32. data/doc/classes/Bio/DB/Sam.src/M000020.html +22 -0
  33. data/doc/classes/Bio/DB/Sam.src/M000021.html +19 -0
  34. data/doc/classes/Bio/DB/Sam.src/M000022.html +25 -0
  35. data/doc/classes/Bio/DB/Sam.src/M000023.html +28 -0
  36. data/doc/classes/Bio/DB/Sam.src/M000024.html +28 -0
  37. data/doc/classes/Bio/DB/Sam.src/M000025.html +46 -0
  38. data/doc/classes/Bio/DB/Sam.src/M000026.html +24 -0
  39. data/doc/classes/Bio/DB/Sam.src/M000027.html +19 -0
  40. data/doc/classes/Bio/DB/Sam.src/M000028.html +24 -0
  41. data/doc/classes/Bio/DB/Sam.src/M000029.html +41 -0
  42. data/doc/classes/Bio/DB/Sam.src/M000030.html +31 -0
  43. data/doc/classes/Bio/DB/Sam.src/M000031.html +86 -0
  44. data/doc/classes/Bio/DB/Sam.src/M000032.html +34 -0
  45. data/doc/classes/Bio/DB/Tag.html +160 -0
  46. data/doc/classes/Bio/DB/Tag.src/M000011.html +21 -0
  47. data/doc/classes/LibC.html +105 -0
  48. data/doc/classes/Pileup.html +374 -0
  49. data/doc/classes/Pileup.src/M000001.html +34 -0
  50. data/doc/classes/Pileup.src/M000002.html +21 -0
  51. data/doc/classes/Pileup.src/M000003.html +21 -0
  52. data/doc/classes/Pileup.src/M000004.html +21 -0
  53. data/doc/classes/Pileup.src/M000005.html +31 -0
  54. data/doc/created.rid +1 -0
  55. data/doc/files/lib/bio-samtools_rb.html +109 -0
  56. data/doc/files/lib/bio/db/sam/bam_rb.html +108 -0
  57. data/doc/files/lib/bio/db/sam/faidx_rb.html +108 -0
  58. data/doc/files/lib/bio/db/sam/library_rb.html +101 -0
  59. data/doc/files/lib/bio/db/sam/pileup_rb.html +178 -0
  60. data/doc/files/lib/bio/db/sam/sam_rb.html +113 -0
  61. data/doc/files/lib/bio/db/sam_rb.html +111 -0
  62. data/doc/fr_class_index.html +43 -0
  63. data/doc/fr_file_index.html +33 -0
  64. data/doc/fr_method_index.html +58 -0
  65. data/doc/index.html +24 -0
  66. data/doc/rdoc-style.css +208 -0
  67. data/doc/tutorial.html +165 -0
  68. data/doc/tutorial.pdf +0 -0
  69. data/lib/bio/db/sam.rb +163 -1
  70. data/lib/bio/db/sam/pileup.rb +98 -0
  71. data/test/basictest.rb +14 -0
  72. data/test/pileup.rb +68 -0
  73. metadata +84 -18
data/README.rdoc CHANGED
@@ -13,27 +13,14 @@ This project was born from the need to add support of BAM files to
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  the gee_fu genome browser (http://github.com/danmaclean/gee_fu).
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  == Installation
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- At the moment, the only way to "install" the module is to copy it to copy the content
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- of the lib folder on any lib folder you have. You must also copy your libbam.a (linux)
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- or libbam.dll (windows) from samtools. If you have a Mac, add the following variable
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- to the makefile of samtools
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-
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- DYFLAGS = -dynamiclib -lz
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-
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- and the following target:
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- dylib: libbam.dylib
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- libbam.dylib:$(LOBJS)
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- $(CC) $(CFLAGS) $(DYFLAGS) -o libbam.dylib $(LOBJS)
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-
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- Then, run
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-
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- make dylib
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-
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- Finally, you copy the .dylib file to your lib folder.
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+ 'gem install bio-samtools'
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  == Usage
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- The easiest way to see in "action" samtools-ruby to call
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- rake test.
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+ The easiest way to see bio-samtools in action is to try the tests
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+ rake basic_test
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+ rake pileup_test
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+
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+ See doc/tutorial.html or doc/tutorial.pdf for a walkthrough tutorial
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  == Dependencies:
@@ -50,9 +37,9 @@ There are two known segmentation faults at the moment
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  If this is not the problem, or you have any other question, don´t hesitate on
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  dropping a line to
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  Ricardo dot Ramirez-Gonzalez at bbsrc dot ac dot uk
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+ dan.maclean@tsl.ac.uk
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  == TODO
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- -Write a gem to install it
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  -Filter to the fetching algorithm (give a condition that has to be satisfied to add the alignment to the list)
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  -Examples of how to use it, besides the test folder
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  -Operating system independent, DONE ( test needed)
data/Rakefile CHANGED
@@ -32,6 +32,17 @@ Jeweler::Tasks.new do |gem|
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  end
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  Jeweler::RubygemsDotOrgTasks.new
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+ desc "Basic Functionality Test"
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+ task :basic_test do
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+ ruby "test/basictest.rb"
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+ end
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+
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+
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+ desc "Test the Pileup class"
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+ task :pileup_test do
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+ ruby "test/pileup.rb"
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+ end
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+
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  require 'rake/testtask'
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  Rake::TestTask.new(:test) do |test|
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  test.libs << 'lib' << 'test'
data/VERSION CHANGED
@@ -1 +1 @@
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- 0.2.5
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+ 0.3.0
data/bio-samtools.gemspec CHANGED
@@ -5,7 +5,7 @@
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  Gem::Specification.new do |s|
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  s.name = %q{bio-samtools}
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- s.version = "0.2.5"
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+ s.version = "0.3.0"
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  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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  s.authors = [%q{Ricardo Ramirez-Gonzalez}, %q{Dan MacLean}, %q{Raoul J.P. Bonnal}]
@@ -29,6 +29,70 @@ Gem::Specification.new do |s|
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  "Rakefile",
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  "VERSION",
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  "bio-samtools.gemspec",
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+ "doc/basic_styles.css",
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+ "doc/classes/Bio.html",
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+ "doc/classes/Bio/DB.html",
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+ "doc/classes/Bio/DB/Alignment.html",
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+ "doc/classes/Bio/DB/Alignment.src/M000012.html",
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+ "doc/classes/Bio/DB/Alignment.src/M000013.html",
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+ "doc/classes/Bio/DB/Alignment.src/M000014.html",
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+ "doc/classes/Bio/DB/Alignment.src/M000015.html",
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+ "doc/classes/Bio/DB/SAM.html",
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+ "doc/classes/Bio/DB/SAM/Library.html",
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+ "doc/classes/Bio/DB/SAM/Library.src/M000006.html",
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+ "doc/classes/Bio/DB/SAM/Tools.html",
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+ "doc/classes/Bio/DB/SAM/Tools.src/M000007.html",
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+ "doc/classes/Bio/DB/SAM/Tools/Bam1CoreT.html",
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+ "doc/classes/Bio/DB/SAM/Tools/Bam1T.html",
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+ "doc/classes/Bio/DB/SAM/Tools/Bam1T.src/M000010.html",
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+ "doc/classes/Bio/DB/SAM/Tools/BamHeaderT.html",
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+ "doc/classes/Bio/DB/SAM/Tools/BamHeaderT.src/M000008.html",
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+ "doc/classes/Bio/DB/SAM/Tools/BamHeaderT.src/M000009.html",
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+ "doc/classes/Bio/DB/SAM/Tools/BamPileup1T.html",
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+ "doc/classes/Bio/DB/SAM/Tools/SamfileT.html",
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+ "doc/classes/Bio/DB/SAM/Tools/SamfileTX.html",
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+ "doc/classes/Bio/DB/SAMException.html",
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+ "doc/classes/Bio/DB/SAMException.src/M000016.html",
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+ "doc/classes/Bio/DB/Sam.src/M000017.html",
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+ "doc/classes/Bio/DB/Sam.src/M000018.html",
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+ "doc/classes/Bio/DB/Sam.src/M000019.html",
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+ "doc/classes/Bio/DB/Sam.src/M000020.html",
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+ "doc/classes/Bio/DB/Sam.src/M000021.html",
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+ "doc/classes/Bio/DB/Sam.src/M000022.html",
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+ "doc/classes/Bio/DB/Sam.src/M000023.html",
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+ "doc/classes/Bio/DB/Sam.src/M000024.html",
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+ "doc/classes/Bio/DB/Sam.src/M000025.html",
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+ "doc/classes/Bio/DB/Sam.src/M000026.html",
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+ "doc/classes/Bio/DB/Sam.src/M000027.html",
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+ "doc/classes/Bio/DB/Sam.src/M000028.html",
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+ "doc/classes/Bio/DB/Sam.src/M000029.html",
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+ "doc/classes/Bio/DB/Sam.src/M000030.html",
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+ "doc/classes/Bio/DB/Sam.src/M000031.html",
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+ "doc/classes/Bio/DB/Sam.src/M000032.html",
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+ "doc/classes/Bio/DB/Tag.html",
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+ "doc/classes/Bio/DB/Tag.src/M000011.html",
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+ "doc/classes/LibC.html",
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+ "doc/classes/Pileup.html",
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+ "doc/classes/Pileup.src/M000001.html",
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+ "doc/classes/Pileup.src/M000002.html",
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+ "doc/classes/Pileup.src/M000003.html",
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+ "doc/classes/Pileup.src/M000004.html",
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+ "doc/classes/Pileup.src/M000005.html",
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+ "doc/created.rid",
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+ "doc/files/lib/bio-samtools_rb.html",
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+ "doc/files/lib/bio/db/sam/bam_rb.html",
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+ "doc/files/lib/bio/db/sam/faidx_rb.html",
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+ "doc/files/lib/bio/db/sam/library_rb.html",
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+ "doc/files/lib/bio/db/sam/pileup_rb.html",
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+ "doc/files/lib/bio/db/sam/sam_rb.html",
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+ "doc/files/lib/bio/db/sam_rb.html",
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+ "doc/fr_class_index.html",
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+ "doc/fr_file_index.html",
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+ "doc/fr_method_index.html",
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+ "doc/index.html",
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+ "doc/rdoc-style.css",
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+ "doc/tutorial.html",
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+ "doc/tutorial.pdf",
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  "ext/mkrf_conf.rb",
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  "lib/bio-samtools.rb",
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  "lib/bio/.DS_Store",
@@ -38,12 +102,14 @@ Gem::Specification.new do |s|
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  "lib/bio/db/sam/external/VERSION",
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  "lib/bio/db/sam/faidx.rb",
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  "lib/bio/db/sam/library.rb",
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+ "lib/bio/db/sam/pileup.rb",
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  "lib/bio/db/sam/sam.rb",
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  "test/basictest.rb",
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  "test/coverage.rb",
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  "test/coverage_plot.rb",
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  "test/feature.rb",
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  "test/helper.rb",
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+ "test/pileup.rb",
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  "test/samples/small/ids2.txt",
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  "test/samples/small/sorted.bam",
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  "test/samples/small/test",
@@ -0,0 +1,31 @@
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+ /*
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+ untitled
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+
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+ Created by macleand on 2011-10-14.
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+ Copyright (c) 2011 Dan MacLean. All rights reserved.
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+ */
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+ #main { margin: 40px 0 60px 0; overflow: hidden; }
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+ #wrap { width: 800px; margin: 0 auto 50px; }
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+ body { font: 12px/20px "Helvetica Neue", Helvetica, Arial, sans-serif; color: #555; font-weight: normal; }
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+ h1 { font-size: 38px; margin: 0 0 10px 0; }
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+ h2 { font-size: 30px; margin: 0 0 10px 0; }
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+ h3 { font-size: 24px; margin: 0 0 10px 0; }
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+ h4 { font-size: 18px; margin: 0 0 10px 0; }
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+ h5 { font-size: 16px; margin: 0 0 5px 0; }
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+ h6 { font-size: 14px; margin: 0 0 5px 0; }
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+ p { margin: 0 0 15px 0; }
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+ a { text-decoration: none; color: #FF7200; }
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+ a:hover { color: #222; }
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+ em { font-style: italic; }
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+ ul { margin: 0 0 15px 15px; list-style-type: circle; }
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+ ol { margin: 15px 0 15px 20px; list-style-type: decimal; }
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+ strong, b { font-weight: bold; }
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+ .hide { display: none; }
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+ #header { padding: 55px 0 0 0; margin: 0 0 40px 0; }
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+ table {border: 1px solid black; text-align:left; padding:5px;}
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+ th
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+ {
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+ background-color:#FF7200;
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+ padding:5px;
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+ }
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+ td {padding: 5px;}
@@ -0,0 +1,139 @@
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
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+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+
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+ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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+ <head>
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+ <title>Module: Bio</title>
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+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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+ <meta http-equiv="Content-Script-Type" content="text/javascript" />
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+ <link rel="stylesheet" href=".././rdoc-style.css" type="text/css" media="screen" />
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+ <script type="text/javascript">
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+ // <![CDATA[
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+
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+ function popupCode( url ) {
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+ window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
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+ }
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+
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+ function toggleCode( id ) {
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+ if ( document.getElementById )
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+ elem = document.getElementById( id );
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+ else if ( document.all )
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+ elem = eval( "document.all." + id );
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+ else
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+ return false;
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+
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+ elemStyle = elem.style;
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+
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+ if ( elemStyle.display != "block" ) {
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+ elemStyle.display = "block"
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+ } else {
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+ elemStyle.display = "none"
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+ }
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+
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+ return true;
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+ }
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+
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+ // Make codeblocks hidden by default
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+ document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
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+
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+ // ]]>
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+ </script>
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+
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+ </head>
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+ <body>
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+
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+
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+
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+ <div id="classHeader">
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+ <table class="header-table">
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+ <tr class="top-aligned-row">
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+ <td><strong>Module</strong></td>
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+ <td class="class-name-in-header">Bio</td>
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+ </tr>
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+ <tr class="top-aligned-row">
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+ <td><strong>In:</strong></td>
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+ <td>
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+ <a href="../files/lib/bio/db/sam/bam_rb.html">
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+ lib/bio/db/sam/bam.rb
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+ </a>
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+ <br />
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+ <a href="../files/lib/bio/db/sam/faidx_rb.html">
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+ lib/bio/db/sam/faidx.rb
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+ </a>
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+ <br />
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+ <a href="../files/lib/bio/db/sam/library_rb.html">
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+ lib/bio/db/sam/library.rb
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+ </a>
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+ <br />
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+ <a href="../files/lib/bio/db/sam/sam_rb.html">
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+ lib/bio/db/sam/sam.rb
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+ </a>
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+ <br />
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+ <a href="../files/lib/bio/db/sam_rb.html">
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+ lib/bio/db/sam.rb
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+ </a>
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+ <br />
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+ </td>
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+ </tr>
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+
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+ </table>
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+ </div>
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+ <!-- banner header -->
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+
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+ <div id="bodyContent">
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+
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+
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+
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+ <div id="contextContent">
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+
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+ <div id="description">
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+ <pre>
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+ sam.rb
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+
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+ Created by Ricardo Ramirez on 3/25/10.
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+ </pre>
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+ <p>
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+ require &#8216;rubygems&#8217; require&#8216;ffi&#8217; require
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+ &#8216;bio/db/sam/bam&#8216;
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+ </p>
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+
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+ </div>
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+
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+
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+ </div>
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+
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+
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+ </div>
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+
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+
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+ <!-- if includes -->
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+
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+ <div id="section">
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+
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+ <div id="class-list">
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+ <h3 class="section-bar">Classes and Modules</h3>
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+
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+ Class <a href="Bio/DB.html" class="link">Bio::DB</a><br />
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+
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+ </div>
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+
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+
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+
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+
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+
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+
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+
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+ <!-- if method_list -->
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+
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+
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+ </div>
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+
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+
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+ <div id="validator-badges">
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+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
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+ </div>
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+
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+ </body>
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+ </html>
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
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+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+
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+ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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+ <head>
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+ <title>Class: Bio::DB</title>
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+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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+ <meta http-equiv="Content-Script-Type" content="text/javascript" />
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+ <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
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+ <script type="text/javascript">
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+ // <![CDATA[
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+
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+ function popupCode( url ) {
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+ window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
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+ }
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+
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+ function toggleCode( id ) {
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+ if ( document.getElementById )
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+ elem = document.getElementById( id );
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+ else if ( document.all )
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+ elem = eval( "document.all." + id );
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+ else
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+ return false;
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+
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+ elemStyle = elem.style;
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+
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+ if ( elemStyle.display != "block" ) {
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+ elemStyle.display = "block"
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+ } else {
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+ elemStyle.display = "none"
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+ }
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+
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+ return true;
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+ }
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+
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+ // Make codeblocks hidden by default
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+ document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
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+
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+ // ]]>
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+ </script>
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+
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+ </head>
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+ <body>
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+
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+
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+
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+ <div id="classHeader">
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+ <table class="header-table">
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+ <tr class="top-aligned-row">
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+ <td><strong>Class</strong></td>
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+ <td class="class-name-in-header">Bio::DB</td>
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+ </tr>
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+ <tr class="top-aligned-row">
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+ <td><strong>In:</strong></td>
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+ <td>
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+ <a href="../../files/lib/bio/db/sam/bam_rb.html">
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+ lib/bio/db/sam/bam.rb
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+ </a>
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+ <br />
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+ <a href="../../files/lib/bio/db/sam/faidx_rb.html">
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+ lib/bio/db/sam/faidx.rb
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+ </a>
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+ <br />
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