bio-samtools 0.2.5 → 0.3.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- data/README.rdoc +7 -20
- data/Rakefile +11 -0
- data/VERSION +1 -1
- data/bio-samtools.gemspec +67 -1
- data/doc/basic_styles.css +31 -0
- data/doc/classes/Bio.html +139 -0
- data/doc/classes/Bio/DB.html +137 -0
- data/doc/classes/Bio/DB/Alignment.html +441 -0
- data/doc/classes/Bio/DB/Alignment.src/M000012.html +19 -0
- data/doc/classes/Bio/DB/Alignment.src/M000013.html +27 -0
- data/doc/classes/Bio/DB/Alignment.src/M000014.html +45 -0
- data/doc/classes/Bio/DB/Alignment.src/M000015.html +40 -0
- data/doc/classes/Bio/DB/SAM.html +510 -0
- data/doc/classes/Bio/DB/SAM/Library.html +135 -0
- data/doc/classes/Bio/DB/SAM/Library.src/M000006.html +28 -0
- data/doc/classes/Bio/DB/SAM/Tools.html +278 -0
- data/doc/classes/Bio/DB/SAM/Tools.src/M000007.html +20 -0
- data/doc/classes/Bio/DB/SAM/Tools/Bam1CoreT.html +111 -0
- data/doc/classes/Bio/DB/SAM/Tools/Bam1T.html +150 -0
- data/doc/classes/Bio/DB/SAM/Tools/Bam1T.src/M000010.html +20 -0
- data/doc/classes/Bio/DB/SAM/Tools/BamHeaderT.html +169 -0
- data/doc/classes/Bio/DB/SAM/Tools/BamHeaderT.src/M000008.html +19 -0
- data/doc/classes/Bio/DB/SAM/Tools/BamHeaderT.src/M000009.html +18 -0
- data/doc/classes/Bio/DB/SAM/Tools/BamPileup1T.html +111 -0
- data/doc/classes/Bio/DB/SAM/Tools/SamfileT.html +129 -0
- data/doc/classes/Bio/DB/SAM/Tools/SamfileTX.html +111 -0
- data/doc/classes/Bio/DB/SAMException.html +140 -0
- data/doc/classes/Bio/DB/SAMException.src/M000016.html +18 -0
- data/doc/classes/Bio/DB/Sam.src/M000017.html +43 -0
- data/doc/classes/Bio/DB/Sam.src/M000018.html +42 -0
- data/doc/classes/Bio/DB/Sam.src/M000019.html +18 -0
- data/doc/classes/Bio/DB/Sam.src/M000020.html +22 -0
- data/doc/classes/Bio/DB/Sam.src/M000021.html +19 -0
- data/doc/classes/Bio/DB/Sam.src/M000022.html +25 -0
- data/doc/classes/Bio/DB/Sam.src/M000023.html +28 -0
- data/doc/classes/Bio/DB/Sam.src/M000024.html +28 -0
- data/doc/classes/Bio/DB/Sam.src/M000025.html +46 -0
- data/doc/classes/Bio/DB/Sam.src/M000026.html +24 -0
- data/doc/classes/Bio/DB/Sam.src/M000027.html +19 -0
- data/doc/classes/Bio/DB/Sam.src/M000028.html +24 -0
- data/doc/classes/Bio/DB/Sam.src/M000029.html +41 -0
- data/doc/classes/Bio/DB/Sam.src/M000030.html +31 -0
- data/doc/classes/Bio/DB/Sam.src/M000031.html +86 -0
- data/doc/classes/Bio/DB/Sam.src/M000032.html +34 -0
- data/doc/classes/Bio/DB/Tag.html +160 -0
- data/doc/classes/Bio/DB/Tag.src/M000011.html +21 -0
- data/doc/classes/LibC.html +105 -0
- data/doc/classes/Pileup.html +374 -0
- data/doc/classes/Pileup.src/M000001.html +34 -0
- data/doc/classes/Pileup.src/M000002.html +21 -0
- data/doc/classes/Pileup.src/M000003.html +21 -0
- data/doc/classes/Pileup.src/M000004.html +21 -0
- data/doc/classes/Pileup.src/M000005.html +31 -0
- data/doc/created.rid +1 -0
- data/doc/files/lib/bio-samtools_rb.html +109 -0
- data/doc/files/lib/bio/db/sam/bam_rb.html +108 -0
- data/doc/files/lib/bio/db/sam/faidx_rb.html +108 -0
- data/doc/files/lib/bio/db/sam/library_rb.html +101 -0
- data/doc/files/lib/bio/db/sam/pileup_rb.html +178 -0
- data/doc/files/lib/bio/db/sam/sam_rb.html +113 -0
- data/doc/files/lib/bio/db/sam_rb.html +111 -0
- data/doc/fr_class_index.html +43 -0
- data/doc/fr_file_index.html +33 -0
- data/doc/fr_method_index.html +58 -0
- data/doc/index.html +24 -0
- data/doc/rdoc-style.css +208 -0
- data/doc/tutorial.html +165 -0
- data/doc/tutorial.pdf +0 -0
- data/lib/bio/db/sam.rb +163 -1
- data/lib/bio/db/sam/pileup.rb +98 -0
- data/test/basictest.rb +14 -0
- data/test/pileup.rb +68 -0
- 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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-
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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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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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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
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rake
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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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See doc/tutorial.html or doc/tutorial.pdf for a walkthrough tutorial
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== Dependencies:
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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)
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data/Rakefile
CHANGED
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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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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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require 'rake/testtask'
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Rake::TestTask.new(:test) do |test|
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test.libs << 'lib' << 'test'
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data/VERSION
CHANGED
@@ -1 +1 @@
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0.
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0.3.0
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data/bio-samtools.gemspec
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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.
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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}]
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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",
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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",
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/*
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untitled
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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;}
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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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<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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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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function toggleCode( id ) {
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elem = eval( "document.all." + id );
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else
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return false;
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elemStyle = elem.style;
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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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return true;
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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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</script>
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</head>
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<body>
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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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