bio-samtools 0.6.2 → 2.0.3
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.
- checksums.yaml +4 -4
- data/Gemfile +3 -2
- data/README.md +4 -7
- data/VERSION +1 -1
- data/bio-samtools.gemspec +47 -105
- data/doc/Bio.html +68 -131
- data/doc/Bio/DB.html +51 -111
- data/doc/Bio/DB/Alignment.html +135 -363
- data/doc/Bio/DB/Pileup.html +183 -170
- data/doc/Bio/DB/SAM.html +1396 -820
- data/doc/Bio/DB/SAM/Library.html +73 -123
- data/doc/Bio/DB/SAM/Tools.html +51 -273
- data/doc/Bio/DB/Tag.html +78 -124
- data/doc/Bio/DB/Vcf.html +111 -147
- data/doc/LICENSE_txt.html +113 -148
- data/doc/created.rid +9 -10
- data/doc/fonts.css +167 -0
- data/doc/fonts/Lato-Light.ttf +0 -0
- data/doc/fonts/Lato-LightItalic.ttf +0 -0
- data/doc/fonts/Lato-Regular.ttf +0 -0
- data/doc/fonts/Lato-RegularItalic.ttf +0 -0
- data/doc/fonts/SourceCodePro-Bold.ttf +0 -0
- data/doc/fonts/SourceCodePro-Regular.ttf +0 -0
- data/doc/images/add.png +0 -0
- data/doc/images/arrow_up.png +0 -0
- data/doc/images/delete.png +0 -0
- data/doc/images/tag_blue.png +0 -0
- data/doc/index.html +48 -54
- data/doc/js/darkfish.js +9 -22
- data/doc/js/search.js +20 -5
- data/doc/js/search_index.js +1 -1
- data/doc/rdoc.css +255 -218
- data/doc/table_of_contents.html +256 -137
- data/ext/Rakefile +57 -0
- data/lib/bio-samtools.rb +7 -2
- data/lib/bio/BIOExtensions.rb +89 -0
- data/lib/bio/db/alignment.rb +59 -0
- data/lib/bio/db/fastadb.rb +255 -0
- data/lib/bio/db/pileup.rb +221 -172
- data/lib/bio/db/sam.rb +639 -589
- data/lib/bio/db/sam/{faidx.rb → faidx_old.rb} +0 -0
- data/lib/bio/db/vcf.rb +69 -68
- data/test/.gitignore +1 -0
- data/test/{test_basic.rb → old_test_basic.rb} +33 -1
- data/test/samples/small/dupes.bam +0 -0
- data/test/samples/small/dupes.sam +274 -0
- data/test/samples/small/map_for_reheader.sam +8 -0
- data/test/samples/small/map_to_merge1.bam +0 -0
- data/test/samples/small/map_to_merge1.bam.bai +0 -0
- data/test/samples/small/map_to_merge1.sam +8 -0
- data/test/samples/small/map_to_merge2.bam +0 -0
- data/test/samples/small/map_to_merge2.bam.bai +0 -0
- data/test/samples/small/map_to_merge2.sam +8 -0
- data/test/samples/small/no_md.sam +8 -0
- data/test/samples/small/test_chr.fasta.1.bt2 +0 -0
- data/test/samples/small/test_chr.fasta.2.bt2 +0 -0
- data/test/samples/small/test_chr.fasta.3.bt2 +0 -0
- data/test/samples/small/test_chr.fasta.4.bt2 +0 -0
- data/test/samples/small/test_chr.fasta.rev.1.bt2 +0 -0
- data/test/samples/small/test_chr.fasta.rev.2.bt2 +0 -0
- data/test/samples/small/test_cov.svg +273 -0
- data/test/samples/small/testu.bam.bai +0 -0
- data/test/svg +133 -0
- data/test/test_pileup.rb +84 -0
- data/test/test_sam.rb +331 -0
- data/test/test_vcf.rb +11 -0
- data/{doc → tutorial}/tutorial.html +0 -0
- data/{doc → tutorial}/tutorial.pdf +0 -0
- metadata +56 -114
- data/doc/Bio/DB/SAM/Tools/Bam1CoreT.html +0 -159
- data/doc/Bio/DB/SAM/Tools/Bam1T.html +0 -220
- data/doc/Bio/DB/SAM/Tools/BamHeaderT.html +0 -249
- data/doc/Bio/DB/SAM/Tools/BamPileup1T.html +0 -159
- data/doc/Bio/DB/SAM/Tools/SamfileT.html +0 -171
- data/doc/Bio/DB/SAM/Tools/SamfileTX.html +0 -159
- data/doc/Bio/DB/SAMException.html +0 -205
- data/doc/LibC.html +0 -155
- data/doc/Pileup.html +0 -571
- data/doc/Vcf.html +0 -473
- data/doc/basic_styles.css +0 -31
- data/doc/classes/Bio.html +0 -139
- data/doc/classes/Bio/DB.html +0 -137
- data/doc/classes/Bio/DB/Alignment.html +0 -441
- data/doc/classes/Bio/DB/Alignment.src/M000012.html +0 -19
- data/doc/classes/Bio/DB/Alignment.src/M000013.html +0 -27
- data/doc/classes/Bio/DB/Alignment.src/M000014.html +0 -45
- data/doc/classes/Bio/DB/Alignment.src/M000015.html +0 -40
- data/doc/classes/Bio/DB/SAM.html +0 -510
- data/doc/classes/Bio/DB/SAM/Library.html +0 -135
- data/doc/classes/Bio/DB/SAM/Library.src/M000006.html +0 -28
- data/doc/classes/Bio/DB/SAM/Tools.html +0 -278
- data/doc/classes/Bio/DB/SAM/Tools.src/M000007.html +0 -20
- data/doc/classes/Bio/DB/SAM/Tools/Bam1CoreT.html +0 -111
- data/doc/classes/Bio/DB/SAM/Tools/Bam1T.html +0 -150
- data/doc/classes/Bio/DB/SAM/Tools/Bam1T.src/M000010.html +0 -20
- data/doc/classes/Bio/DB/SAM/Tools/BamHeaderT.html +0 -169
- data/doc/classes/Bio/DB/SAM/Tools/BamHeaderT.src/M000008.html +0 -19
- data/doc/classes/Bio/DB/SAM/Tools/BamHeaderT.src/M000009.html +0 -18
- data/doc/classes/Bio/DB/SAM/Tools/BamPileup1T.html +0 -111
- data/doc/classes/Bio/DB/SAM/Tools/SamfileT.html +0 -129
- data/doc/classes/Bio/DB/SAM/Tools/SamfileTX.html +0 -111
- data/doc/classes/Bio/DB/SAMException.html +0 -140
- data/doc/classes/Bio/DB/SAMException.src/M000016.html +0 -18
- data/doc/classes/Bio/DB/Sam.src/M000017.html +0 -43
- data/doc/classes/Bio/DB/Sam.src/M000018.html +0 -42
- data/doc/classes/Bio/DB/Sam.src/M000019.html +0 -18
- data/doc/classes/Bio/DB/Sam.src/M000020.html +0 -22
- data/doc/classes/Bio/DB/Sam.src/M000021.html +0 -19
- data/doc/classes/Bio/DB/Sam.src/M000022.html +0 -25
- data/doc/classes/Bio/DB/Sam.src/M000023.html +0 -28
- data/doc/classes/Bio/DB/Sam.src/M000024.html +0 -28
- data/doc/classes/Bio/DB/Sam.src/M000025.html +0 -46
- data/doc/classes/Bio/DB/Sam.src/M000026.html +0 -24
- data/doc/classes/Bio/DB/Sam.src/M000027.html +0 -19
- data/doc/classes/Bio/DB/Sam.src/M000028.html +0 -24
- data/doc/classes/Bio/DB/Sam.src/M000029.html +0 -41
- data/doc/classes/Bio/DB/Sam.src/M000030.html +0 -31
- data/doc/classes/Bio/DB/Sam.src/M000031.html +0 -86
- data/doc/classes/Bio/DB/Sam.src/M000032.html +0 -34
- data/doc/classes/Bio/DB/Tag.html +0 -160
- data/doc/classes/Bio/DB/Tag.src/M000011.html +0 -21
- data/doc/classes/LibC.html +0 -105
- data/doc/classes/Pileup.html +0 -374
- data/doc/classes/Pileup.src/M000001.html +0 -34
- data/doc/classes/Pileup.src/M000002.html +0 -21
- data/doc/classes/Pileup.src/M000003.html +0 -21
- data/doc/classes/Pileup.src/M000004.html +0 -21
- data/doc/classes/Pileup.src/M000005.html +0 -31
- data/doc/files/lib/bio-samtools_rb.html +0 -109
- data/doc/files/lib/bio/db/sam/bam_rb.html +0 -108
- data/doc/files/lib/bio/db/sam/faidx_rb.html +0 -108
- data/doc/files/lib/bio/db/sam/library_rb.html +0 -101
- data/doc/files/lib/bio/db/sam/pileup_rb.html +0 -178
- data/doc/files/lib/bio/db/sam/sam_rb.html +0 -113
- data/doc/files/lib/bio/db/sam_rb.html +0 -111
- data/doc/fr_class_index.html +0 -43
- data/doc/fr_file_index.html +0 -33
- data/doc/fr_method_index.html +0 -58
- data/doc/lib/bio-samtools_rb.html +0 -115
- data/doc/lib/bio/db/pileup_rb.html +0 -171
- data/doc/lib/bio/db/sam/bam_rb.html +0 -121
- data/doc/lib/bio/db/sam/faidx_rb.html +0 -117
- data/doc/lib/bio/db/sam/library_rb.html +0 -115
- data/doc/lib/bio/db/sam/pileup_rb.html +0 -171
- data/doc/lib/bio/db/sam/sam_rb.html +0 -121
- data/doc/lib/bio/db/sam/vcf_rb.html +0 -124
- data/doc/lib/bio/db/sam_rb.html +0 -115
- data/doc/lib/bio/db/vcf_rb.html +0 -124
- data/doc/rdoc-style.css +0 -208
- data/lib/bio/db/sam/bam.rb +0 -210
- data/lib/bio/db/sam/sam.rb +0 -86
- data/test/samples/pipe_char/test.bam +0 -0
- data/test/samples/pipe_char/test.bam.bai +0 -0
- data/test/samples/pipe_char/test.tam +0 -10
- data/test/samples/pipe_char/test_chr.fasta +0 -1000
- data/test/samples/pipe_char/test_chr.fasta.fai +0 -1
- data/test/samples/small/test +0 -0
- data/test/samples/small/test.bam +0 -0
- data/test/samples/small/test.fa +0 -20
- data/test/samples/small/test.fai +0 -0
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<pre><span class="ruby-comment cmt"># File lib/bio/db/sam/pileup.rb, line 34</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">pile_up_line</span>)
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<span class="ruby-identifier">cols</span> = <span class="ruby-identifier">pile_up_line</span>.<span class="ruby-identifier">split</span>(<span class="ruby-regexp re">/\t/</span>)
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<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">cols</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">==</span> <span class="ruby-value">6</span> <span class="ruby-comment cmt">##should only be able to get 6 lines from mpileup</span>
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<span class="ruby-ivar">@ref_name</span>, <span class="ruby-ivar">@pos</span>, <span class="ruby-ivar">@ref_base</span>, <span class="ruby-ivar">@coverage</span>, <span class="ruby-ivar">@read_bases</span>, <span class="ruby-ivar">@read_quals</span> = <span class="ruby-identifier">cols</span>
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<span class="ruby-keyword kw">elsif</span> (<span class="ruby-value">10</span><span class="ruby-operator">..</span><span class="ruby-value">13</span>).<span class="ruby-identifier">include?</span>(<span class="ruby-identifier">cols</span>.<span class="ruby-identifier">length</span>) <span class="ruby-comment cmt">##incase anyone tries to use deprecated pileup with -c flag we get upto 13 cols...</span>
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<span class="ruby-ivar">@ref_name</span>, <span class="ruby-ivar">@pos</span>, <span class="ruby-ivar">@ref_base</span>, <span class="ruby-ivar">@consensus</span>, <span class="ruby-ivar">@consensus_quality</span>, <span class="ruby-ivar">@snp_quality</span>, <span class="ruby-ivar">@rms_mapq</span>, <span class="ruby-ivar">@coverage</span>, <span class="ruby-ivar">@read_bases</span>, <span class="ruby-ivar">@read_quals</span>, <span class="ruby-ivar">@ar1</span>, <span class="ruby-ivar">@ar2</span>, <span class="ruby-ivar">@ar3</span> = <span class="ruby-identifier">cols</span>
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<span class="ruby-ivar">@consensus_quality</span> = <span class="ruby-ivar">@consensus_quality</span>.<span class="ruby-identifier">to_f</span>
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<span class="ruby-ivar">@snp_quality</span> = <span class="ruby-ivar">@snp_quality</span>.<span class="ruby-identifier">to_f</span>
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<span class="ruby-ivar">@rms_mapq</span> = <span class="ruby-ivar">@rms_mapq</span>.<span class="ruby-identifier">to_f</span>
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<span class="ruby-keyword kw">else</span>
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<span class="ruby-comment cmt">#raise RuntimeError, "parsing line '#{pile_up_line.chomp}' failed"</span>
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<span class="ruby-ivar">@pos</span> = <span class="ruby-ivar">@pos</span>.<span class="ruby-identifier">to_i</span>
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<span class="ruby-ivar">@coverage</span> = <span class="ruby-ivar">@coverage</span>.<span class="ruby-identifier">to_f</span>
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<span class="ruby-ivar">@ref_count</span> = <span class="ruby-keyword kw">nil</span>
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<span class="ruby-ivar">@non_ref_count_hash</span> = <span class="ruby-keyword kw">nil</span>
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<span class="ruby-ivar">@non_ref_count</span> = <span class="ruby-keyword kw">nil</span>
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<span class="ruby-keyword kw">end</span></pre>
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<pre><span class="ruby-comment cmt"># File lib/bio/db/sam/pileup.rb, line 56</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">non_refs</span>
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<span class="ruby-ivar">@non_ref_count_hash</span> = {<span class="ruby-identifier">:A</span> =<span class="ruby-operator">></span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">read_bases</span>.<span class="ruby-identifier">count</span>(<span class="ruby-value str">"Aa"</span>), <span class="ruby-identifier">:C</span> =<span class="ruby-operator">></span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">read_bases</span>.<span class="ruby-identifier">count</span>(<span class="ruby-value str">"Cc"</span>), <span class="ruby-identifier">:G</span> =<span class="ruby-operator">></span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">read_bases</span>.<span class="ruby-identifier">count</span>(<span class="ruby-value str">"Gg"</span>), <span class="ruby-identifier">:T</span> =<span class="ruby-operator">></span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">read_bases</span>.<span class="ruby-identifier">count</span>(<span class="ruby-value str">"Tt"</span>)}
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<pre><span class="ruby-comment cmt"># File lib/bio/db/sam/pileup.rb, line 64</span>
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<span class="ruby-ivar">@non_ref_count</span> = <span class="ruby-ivar">@read_bases</span>.<span class="ruby-identifier">count</span>(<span class="ruby-value str">"ATGCatgc"</span>).<span class="ruby-identifier">to_f</span>
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<span class="ruby-ivar">@ref_count</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">read_bases</span>.<span class="ruby-identifier">count</span>(<span class="ruby-value str">".,"</span>)
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<p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
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