bio-samtools 0.4.1 → 0.4.2
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- data/VERSION +1 -1
- data/bio-samtools.gemspec +60 -6
- data/doc/Bio.html +171 -0
- data/doc/Bio/DB.html +163 -0
- data/doc/Bio/DB/Alignment.html +780 -0
- data/doc/Bio/DB/SAM.html +1241 -0
- data/doc/Bio/DB/SAM/Library.html +217 -0
- data/doc/Bio/DB/SAM/Tools.html +331 -0
- data/doc/Bio/DB/SAM/Tools/Bam1CoreT.html +159 -0
- data/doc/Bio/DB/SAM/Tools/Bam1T.html +220 -0
- data/doc/Bio/DB/SAM/Tools/BamHeaderT.html +249 -0
- data/doc/Bio/DB/SAM/Tools/BamPileup1T.html +159 -0
- data/doc/Bio/DB/SAM/Tools/SamfileT.html +171 -0
- data/doc/Bio/DB/SAM/Tools/SamfileTX.html +159 -0
- data/doc/Bio/DB/SAMException.html +205 -0
- data/doc/Bio/DB/Tag.html +254 -0
- data/doc/LICENSE_txt.html +881 -0
- data/doc/LibC.html +153 -0
- data/doc/Pileup.html +571 -0
- data/doc/Vcf.html +473 -0
- data/doc/created.rid +10 -1
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- data/doc/images/wrench_orange.png +0 -0
- data/doc/images/zoom.png +0 -0
- data/doc/index.html +109 -21
- data/doc/js/darkfish.js +153 -0
- data/doc/js/jquery.js +18 -0
- data/doc/js/navigation.js +142 -0
- data/doc/js/search.js +94 -0
- data/doc/js/search_index.js +1 -0
- data/doc/js/searcher.js +228 -0
- data/doc/lib/bio-samtools_rb.html +115 -0
- data/doc/lib/bio/db/sam/bam_rb.html +121 -0
- data/doc/lib/bio/db/sam/faidx_rb.html +117 -0
- data/doc/lib/bio/db/sam/library_rb.html +115 -0
- data/doc/lib/bio/db/sam/pileup_rb.html +171 -0
- data/doc/lib/bio/db/sam/sam_rb.html +121 -0
- data/doc/lib/bio/db/sam/vcf_rb.html +124 -0
- data/doc/lib/bio/db/sam_rb.html +115 -0
- data/doc/rdoc.css +543 -0
- data/doc/table_of_contents.html +186 -0
- data/ext/Makefile-bioruby.patch +1 -1
- data/ext/Rakefile +8 -1
- data/ext/mkrf_conf.rb +8 -1
- data/lib/bio/db/sam.rb +140 -27
- data/lib/bio/db/sam/vcf.rb +0 -1
- data/test/basictest.rb +4 -4
- data/test/test_basic.rb +50 -34
- metadata +79 -25
- data/test/coverage.rb +0 -26
- data/test/coverage_plot.rb +0 -28
- data/test/feature.rb +0 -0
- data/test/test_pileup.rb +0 -68
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<h1 class="class">class Bio::DB::SAM::Tools::SamfileT</h1>
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<div id="description" class="description">
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