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
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<title>mpileup (Bio::DB::Sam)</title>
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<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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<pre><span class="ruby-comment cmt"># File lib/bio/db/sam.rb, line 279</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">mpileup</span>( <span class="ruby-identifier">opts</span> )
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<span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-value str">"No BAMFile provided"</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-ivar">@sam</span> <span class="ruby-keyword kw">and</span> <span class="ruby-ivar">@binary</span>
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<span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-value str">"No FastA provided"</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-ivar">@fasta_path</span>
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<span class="ruby-comment cmt">#long option form to short samtools form..</span>
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<span class="ruby-identifier">long_opts</span> = {
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<span class="ruby-identifier">:region</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">:r</span>,
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<span class="ruby-identifier">:illumina_quals</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">:six</span>,
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<span class="ruby-identifier">:count_anomalous</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">:A</span>,
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<span class="ruby-identifier">:no_baq</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">:B</span>,
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<span class="ruby-identifier">:adjust_mapq</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">:C</span>,
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<span class="ruby-identifier">:max_per_bam_depth</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">:d</span>,
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<span class="ruby-identifier">:extended_baq</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">:E</span>,
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<span class="ruby-identifier">:exclude_reads_file</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">:G</span>,
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<span class="ruby-identifier">:list_of_positions</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">:l</span>,
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<span class="ruby-identifier">:mapping_quality_cap</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">:M</span>,
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<span class="ruby-identifier">:ignore_rg</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">:R</span>,
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<span class="ruby-identifier">:min_mapping_quality</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">:q</span>,
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<span class="ruby-identifier">:min_base_quality</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">:Q</span>
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}
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<span class="ruby-comment cmt">##convert any long_opts to short opts </span>
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<span class="ruby-identifier">opts</span>.<span class="ruby-identifier">each_pair</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">k</span>,<span class="ruby-identifier">v</span><span class="ruby-operator">|</span>
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<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">long_opts</span>[<span class="ruby-identifier">k</span>]
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<span class="ruby-identifier">opts</span>[<span class="ruby-identifier">long_opts</span>[<span class="ruby-identifier">k</span>]] = <span class="ruby-identifier">v</span>
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<span class="ruby-identifier">opts</span>.<span class="ruby-identifier">delete</span>(<span class="ruby-identifier">k</span>)
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-comment cmt">##remove any calls to -g or -u for mpileup, bcf output is not yet supported</span>
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<span class="ruby-comment cmt">##and also associated output options</span>
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[<span class="ruby-identifier">:g</span>, <span class="ruby-identifier">:u</span>, <span class="ruby-identifier">:e</span>, <span class="ruby-identifier">:h</span>, <span class="ruby-identifier">:I</span>, <span class="ruby-identifier">:L</span>, <span class="ruby-identifier">:o</span>, <span class="ruby-identifier">:p</span>].<span class="ruby-identifier">each</span> {<span class="ruby-operator">|</span><span class="ruby-identifier">x</span><span class="ruby-operator">|</span> <span class="ruby-identifier">opts</span>.<span class="ruby-identifier">delete</span>(<span class="ruby-identifier">x</span>) }
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<span class="ruby-identifier">strptrs</span> = []
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<span class="ruby-identifier">strptrs</span> <span class="ruby-operator"><<</span> <span class="ruby-constant">FFI</span><span class="ruby-operator">::</span><span class="ruby-constant">MemoryPointer</span>.<span class="ruby-identifier">from_string</span>(<span class="ruby-value str">"mpileup"</span>)
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<span class="ruby-identifier">opts</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">k</span>,<span class="ruby-identifier">v</span><span class="ruby-operator">|</span>
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<span class="ruby-keyword kw">next</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">opts</span>[<span class="ruby-identifier">k</span>] <span class="ruby-comment cmt">##dont bother unless the values provided are true.. </span>
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<span class="ruby-identifier">k</span> = <span class="ruby-value str">'6'</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">k</span> <span class="ruby-operator">==</span> <span class="ruby-identifier">:six</span>
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<span class="ruby-identifier">k</span> = <span class="ruby-value str">'-'</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">k</span>.<span class="ruby-identifier">to_s</span>
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<span class="ruby-identifier">strptrs</span> <span class="ruby-operator"><<</span> <span class="ruby-constant">FFI</span><span class="ruby-operator">::</span><span class="ruby-constant">MemoryPointer</span>.<span class="ruby-identifier">from_string</span>(<span class="ruby-identifier">k</span>)
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<span class="ruby-identifier">strptrs</span> <span class="ruby-operator"><<</span> <span class="ruby-constant">FFI</span><span class="ruby-operator">::</span><span class="ruby-constant">MemoryPointer</span>.<span class="ruby-identifier">from_string</span>(<span class="ruby-identifier">v</span>.<span class="ruby-identifier">to_s</span>) <span class="ruby-keyword kw">unless</span> [<span class="ruby-value str">"-R"</span>, <span class="ruby-value str">"-B"</span>, <span class="ruby-value str">"-E"</span>, <span class="ruby-value str">"-6"</span>, <span class="ruby-value str">"-A"</span>].<span class="ruby-identifier">include?</span>(<span class="ruby-identifier">k</span>) <span class="ruby-comment cmt">#these are just flags so don't pass a value...</span>
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-identifier">strptrs</span> <span class="ruby-operator"><<</span> <span class="ruby-constant">FFI</span><span class="ruby-operator">::</span><span class="ruby-constant">MemoryPointer</span>.<span class="ruby-identifier">from_string</span>(<span class="ruby-value str">'-f'</span>)
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<span class="ruby-identifier">strptrs</span> <span class="ruby-operator"><<</span> <span class="ruby-constant">FFI</span><span class="ruby-operator">::</span><span class="ruby-constant">MemoryPointer</span>.<span class="ruby-identifier">from_string</span>(<span class="ruby-ivar">@fasta_path</span>)
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<span class="ruby-identifier">strptrs</span> <span class="ruby-operator"><<</span> <span class="ruby-constant">FFI</span><span class="ruby-operator">::</span><span class="ruby-constant">MemoryPointer</span>.<span class="ruby-identifier">from_string</span>(<span class="ruby-ivar">@sam</span>)
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<span class="ruby-identifier">strptrs</span> <span class="ruby-operator"><<</span> <span class="ruby-keyword kw">nil</span>
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<span class="ruby-comment cmt"># Now load all the pointers into a native memory block</span>
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<span class="ruby-identifier">argv</span> = <span class="ruby-constant">FFI</span><span class="ruby-operator">::</span><span class="ruby-constant">MemoryPointer</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">:pointer</span>, <span class="ruby-identifier">strptrs</span>.<span class="ruby-identifier">length</span>)
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<span class="ruby-identifier">strptrs</span>.<span class="ruby-identifier">each_with_index</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">p</span>, <span class="ruby-identifier">i</span><span class="ruby-operator">|</span>
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<span class="ruby-identifier">argv</span>[<span class="ruby-identifier">i</span>].<span class="ruby-identifier">put_pointer</span>(<span class="ruby-value">0</span>, <span class="ruby-identifier">p</span>)
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-identifier">old_stdout</span> = <span class="ruby-constant">STDOUT</span>.<span class="ruby-identifier">clone</span>
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<span class="ruby-identifier">read_pipe</span>, <span class="ruby-identifier">write_pipe</span> = <span class="ruby-constant">IO</span>.<span class="ruby-identifier">pipe</span>()
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<span class="ruby-constant">STDOUT</span>.<span class="ruby-identifier">reopen</span>(<span class="ruby-identifier">write_pipe</span>)
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<span class="ruby-comment cmt">#int bam_mpileup(int argc, char *argv[])</span>
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<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">DB</span><span class="ruby-operator">::</span><span class="ruby-constant">SAM</span><span class="ruby-operator">::</span><span class="ruby-constant">Tools</span>.<span class="ruby-identifier">bam_mpileup</span>(<span class="ruby-identifier">strptrs</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">-</span> <span class="ruby-value">1</span>,<span class="ruby-identifier">argv</span>)
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<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">fork</span>
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<span class="ruby-identifier">write_pipe</span>.<span class="ruby-identifier">close</span>
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<span class="ruby-constant">STDOUT</span>.<span class="ruby-identifier">reopen</span>(<span class="ruby-identifier">old_stdout</span>) <span class="ruby-comment cmt">#beware .. stdout from other processes eg tests calling this method can get mixed in...</span>
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<span class="ruby-keyword kw">begin</span>
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<span class="ruby-keyword kw">while</span> <span class="ruby-identifier">line</span> = <span class="ruby-identifier">read_pipe</span>.<span class="ruby-identifier">readline</span>
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<span class="ruby-keyword kw">yield</span> <span class="ruby-constant">Pileup</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">line</span>)
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-keyword kw">rescue</span> <span class="ruby-constant">EOFError</span>
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<span class="ruby-identifier">read_pipe</span>.<span class="ruby-identifier">close</span>
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<span class="ruby-constant">Process</span>.<span class="ruby-identifier">wait</span>
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-keyword kw">end</span></pre>
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<title>deprecated_pileup (Bio::DB::Sam)</title>
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<pre><span class="ruby-comment cmt"># File lib/bio/db/sam.rb, line 357</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">deprecated_pileup</span>( <span class="ruby-identifier">cmd</span> )
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<span class="ruby-identifier">system</span>(<span class="ruby-value str">'samtools pileup > /dev/null 2>&1'</span>)
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<span class="ruby-comment cmt">##assumes samtools is in the path...</span>
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<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">$?</span>.<span class="ruby-identifier">exitstatus</span> <span class="ruby-operator">></span> <span class="ruby-value">1</span>
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<span class="ruby-identifier">raise</span> <span class="ruby-constant">RuntimeError</span>, <span class="ruby-value str">"samtools is required on the path. A version of samtools with the pileup function is required"</span>
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-value str">"No BAMFile provided"</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-ivar">@sam</span> <span class="ruby-keyword kw">and</span> <span class="ruby-ivar">@binary</span>
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<span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-value str">"No FastA provided"</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-ivar">@fasta_path</span>
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<span class="ruby-identifier">command</span> = <span class="ruby-value str">'samtools pileup '</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">cmd</span> <span class="ruby-operator">+</span> <span class="ruby-node">" -f #{@fasta_path}"</span> <span class="ruby-operator">+</span> <span class="ruby-node">" #{@sam}"</span>
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<span class="ruby-identifier">pipe</span> = <span class="ruby-constant">IO</span>.<span class="ruby-identifier">popen</span>(<span class="ruby-identifier">command</span>)
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<span class="ruby-keyword kw">while</span> <span class="ruby-identifier">line</span> = <span class="ruby-identifier">pipe</span>.<span class="ruby-identifier">gets</span>
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<span class="ruby-keyword kw">yield</span> <span class="ruby-constant">Pileup</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">line</span>)
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-identifier">pipe</span>.<span class="ruby-identifier">close</span>
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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/pileup_rb.html">
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lib/bio/db/sam/pileup.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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<tr class="top-aligned-row">
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<td><strong>Parent:</strong></td>
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<td>
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Object
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</td>
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</tr>
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</table>
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</div>
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<!-- banner header -->
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<div id="bodyContent">
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<div id="contextContent">
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<div id="description">
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<h1><a href="Pileup.html">Pileup</a></h1>
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<p>
|
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A class representing information in SAMTools pileup format
|
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</p>
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<table>
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<tr><td valign="top">Author:</td><td>Dan MacLean (dan.maclean@tsl.ac.uk)
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</td></tr>
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</table>
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<p>
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<a href="Pileup.html">Pileup</a> is described at <a
|
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href="http://sourceforge.net/apps/mediawiki/samtools/index.php?title=SAM_FAQ#I_do_not_understand_the_columns_in_the_pileup_output">sourceforge.net/apps/mediawiki/samtools/index.php?title=SAM_FAQ#I_do_not_understand_the_columns_in_the_pileup_output</a>.
|
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Briefly (when you invoke pileup with the -c option):
|
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+
</p>
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<ul>
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<li>1 reference sequence name
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+
|
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99
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</li>
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<li>2 reference coordinate
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+
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</li>
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<li>(3) reference base, or `*’ for an indel line
|
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+
|
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</li>
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<li>(4) genotype where heterozygotes are encoded in the IUB code: M=A/C, R=A/G,
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W=A/T, S=C/G, Y=C/T and K=G/T; indels are indicated by, for example, */+A,
|
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-A/* or +CC/-C. There is no difference between */+A or +A/*.
|
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+
|
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</li>
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|
+
<li>(5) Phred-scaled likelihood that the genotype is wrong, which is also
|
|
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|
+
called `<a href="Pileup.html#M000005">consensus</a> quality’.
|
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|
+
|
|
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|
+
</li>
|
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|
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<li>(6) Phred-scaled likelihood that the genotype is identical to the
|
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|
+
reference, which is also called `SNP quality’. Suppose the reference
|
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117
|
+
base is A and in alignment we see 17 G and 3 A. We will get a low <a
|
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|
+
href="Pileup.html#M000005">consensus</a> quality because it is difficult to
|
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|
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distinguish an A/G heterozygote from a G/G homozygote. We will get a high
|
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|
+
SNP quality, though, because the evidence of a SNP is very strong.
|
|
121
|
+
|
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122
|
+
</li>
|
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123
|
+
<li>(7) root mean square (RMS) mapping quality
|
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124
|
+
|
|
125
|
+
</li>
|
|
126
|
+
<li>8 # reads covering the position
|
|
127
|
+
|
|
128
|
+
</li>
|
|
129
|
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<li>9 read bases at a SNP line (check the manual page for more information);
|
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|
+
the 1st indel allele otherwise
|
|
131
|
+
|
|
132
|
+
</li>
|
|
133
|
+
<li>10 base quality at a SNP line; the 2nd indel allele otherwise
|
|
134
|
+
|
|
135
|
+
</li>
|
|
136
|
+
<li>(11) indel line only: # reads directly supporting the 1st indel allele
|
|
137
|
+
|
|
138
|
+
</li>
|
|
139
|
+
<li>(12) indel line only: # reads directly supporting the 2nd indel allele
|
|
140
|
+
|
|
141
|
+
</li>
|
|
142
|
+
<li>(13) indel line only: # reads supporting a third indel allele
|
|
143
|
+
|
|
144
|
+
</li>
|
|
145
|
+
</ul>
|
|
146
|
+
<p>
|
|
147
|
+
If pileup is invoked without `-c’, indel lines and columns between 3
|
|
148
|
+
and 7 inclusive will not be outputted.
|
|
149
|
+
</p>
|
|
150
|
+
<p>
|
|
151
|
+
NB mpileup uses the 6 column output format eg
|
|
152
|
+
"seq2\t151\tG\tG\t36\t0\t99\t12\t...........A\t:9<;;7=<<<<<"
|
|
153
|
+
<a href="Pileup.html">Pileup</a> provides accessors for all columns (6 or
|
|
154
|
+
10 column format) and a few other useful methods
|
|
155
|
+
</p>
|
|
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|
+
|
|
157
|
+
</div>
|
|
158
|
+
|
|
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|
+
|
|
160
|
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</div>
|
|
161
|
+
|
|
162
|
+
<div id="method-list">
|
|
163
|
+
<h3 class="section-bar">Methods</h3>
|
|
164
|
+
|
|
165
|
+
<div class="name-list">
|
|
166
|
+
<a href="#M000005">consensus</a>
|
|
167
|
+
<a href="#M000001">new</a>
|
|
168
|
+
<a href="#M000003">non_ref_count</a>
|
|
169
|
+
<a href="#M000002">non_refs</a>
|
|
170
|
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<a href="#M000004">ref_count</a>
|
|
171
|
+
</div>
|
|
172
|
+
</div>
|
|
173
|
+
|
|
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|
+
</div>
|
|
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|
+
|
|
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|
+
|
|
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|
+
<!-- if includes -->
|
|
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|
+
|
|
179
|
+
<div id="section">
|
|
180
|
+
|
|
181
|
+
|
|
182
|
+
|
|
183
|
+
|
|
184
|
+
|
|
185
|
+
<div id="attribute-list">
|
|
186
|
+
<h3 class="section-bar">Attributes</h3>
|
|
187
|
+
|
|
188
|
+
<div class="name-list">
|
|
189
|
+
<table>
|
|
190
|
+
<tr class="top-aligned-row context-row">
|
|
191
|
+
<td class="context-item-name">ar1</td>
|
|
192
|
+
<td class="context-item-value"> [RW] </td>
|
|
193
|
+
<td class="context-item-desc"></td>
|
|
194
|
+
</tr>
|
|
195
|
+
<tr class="top-aligned-row context-row">
|
|
196
|
+
<td class="context-item-name">ar2</td>
|
|
197
|
+
<td class="context-item-value"> [RW] </td>
|
|
198
|
+
<td class="context-item-desc"></td>
|
|
199
|
+
</tr>
|
|
200
|
+
<tr class="top-aligned-row context-row">
|
|
201
|
+
<td class="context-item-name">ar3</td>
|
|
202
|
+
<td class="context-item-value"> [RW] </td>
|
|
203
|
+
<td class="context-item-desc"></td>
|
|
204
|
+
</tr>
|
|
205
|
+
<tr class="top-aligned-row context-row">
|
|
206
|
+
<td class="context-item-name">consensus</td>
|
|
207
|
+
<td class="context-item-value"> [RW] </td>
|
|
208
|
+
<td class="context-item-desc"></td>
|
|
209
|
+
</tr>
|
|
210
|
+
<tr class="top-aligned-row context-row">
|
|
211
|
+
<td class="context-item-name">consensus_quality</td>
|
|
212
|
+
<td class="context-item-value"> [RW] </td>
|
|
213
|
+
<td class="context-item-desc"></td>
|
|
214
|
+
</tr>
|
|
215
|
+
<tr class="top-aligned-row context-row">
|
|
216
|
+
<td class="context-item-name">coverage</td>
|
|
217
|
+
<td class="context-item-value"> [RW] </td>
|
|
218
|
+
<td class="context-item-desc"></td>
|
|
219
|
+
</tr>
|
|
220
|
+
<tr class="top-aligned-row context-row">
|
|
221
|
+
<td class="context-item-name">pos</td>
|
|
222
|
+
<td class="context-item-value"> [RW] </td>
|
|
223
|
+
<td class="context-item-desc"></td>
|
|
224
|
+
</tr>
|
|
225
|
+
<tr class="top-aligned-row context-row">
|
|
226
|
+
<td class="context-item-name">read_bases</td>
|
|
227
|
+
<td class="context-item-value"> [RW] </td>
|
|
228
|
+
<td class="context-item-desc"></td>
|
|
229
|
+
</tr>
|
|
230
|
+
<tr class="top-aligned-row context-row">
|
|
231
|
+
<td class="context-item-name">read_quals</td>
|
|
232
|
+
<td class="context-item-value"> [RW] </td>
|
|
233
|
+
<td class="context-item-desc"></td>
|
|
234
|
+
</tr>
|
|
235
|
+
<tr class="top-aligned-row context-row">
|
|
236
|
+
<td class="context-item-name">ref_base</td>
|
|
237
|
+
<td class="context-item-value"> [RW] </td>
|
|
238
|
+
<td class="context-item-desc"></td>
|
|
239
|
+
</tr>
|
|
240
|
+
<tr class="top-aligned-row context-row">
|
|
241
|
+
<td class="context-item-name">ref_name</td>
|
|
242
|
+
<td class="context-item-value"> [RW] </td>
|
|
243
|
+
<td class="context-item-desc"></td>
|
|
244
|
+
</tr>
|
|
245
|
+
<tr class="top-aligned-row context-row">
|
|
246
|
+
<td class="context-item-name">rms_mapq</td>
|
|
247
|
+
<td class="context-item-value"> [RW] </td>
|
|
248
|
+
<td class="context-item-desc"></td>
|
|
249
|
+
</tr>
|
|
250
|
+
<tr class="top-aligned-row context-row">
|
|
251
|
+
<td class="context-item-name">snp_quality</td>
|
|
252
|
+
<td class="context-item-value"> [RW] </td>
|
|
253
|
+
<td class="context-item-desc"></td>
|
|
254
|
+
</tr>
|
|
255
|
+
</table>
|
|
256
|
+
</div>
|
|
257
|
+
</div>
|
|
258
|
+
|
|
259
|
+
|
|
260
|
+
|
|
261
|
+
<!-- if method_list -->
|
|
262
|
+
<div id="methods">
|
|
263
|
+
<h3 class="section-bar">Public Class methods</h3>
|
|
264
|
+
|
|
265
|
+
<div id="method-M000001" class="method-detail">
|
|
266
|
+
<a name="M000001"></a>
|
|
267
|
+
|
|
268
|
+
<div class="method-heading">
|
|
269
|
+
<a href="Pileup.src/M000001.html" target="Code" class="method-signature"
|
|
270
|
+
onclick="popupCode('Pileup.src/M000001.html');return false;">
|
|
271
|
+
<span class="method-name">new</span><span class="method-args">(pile_up_line)</span>
|
|
272
|
+
</a>
|
|
273
|
+
</div>
|
|
274
|
+
|
|
275
|
+
<div class="method-description">
|
|
276
|
+
<p>
|
|
277
|
+
creates the <a href="Pileup.html">Pileup</a> object
|
|
278
|
+
</p>
|
|
279
|
+
<pre>
|
|
280
|
+
pile_up_line = "seq2\t151\tG\tG\t36\t0\t99\t12\t...........A\t:9<;;7=<<<<<"
|
|
281
|
+
pile = Pileup.new(pile_up_line)
|
|
282
|
+
</pre>
|
|
283
|
+
</div>
|
|
284
|
+
</div>
|
|
285
|
+
|
|
286
|
+
<h3 class="section-bar">Public Instance methods</h3>
|
|
287
|
+
|
|
288
|
+
<div id="method-M000005" class="method-detail">
|
|
289
|
+
<a name="M000005"></a>
|
|
290
|
+
|
|
291
|
+
<div class="method-heading">
|
|
292
|
+
<a href="Pileup.src/M000005.html" target="Code" class="method-signature"
|
|
293
|
+
onclick="popupCode('Pileup.src/M000005.html');return false;">
|
|
294
|
+
<span class="method-name">consensus</span><span class="method-args">()</span>
|
|
295
|
+
</a>
|
|
296
|
+
</div>
|
|
297
|
+
|
|
298
|
+
<div class="method-description">
|
|
299
|
+
<p>
|
|
300
|
+
returns the <a href="Pileup.html#M000005">consensus</a> (most frequent)
|
|
301
|
+
base from the pileup, if there are equally represented bases returns a
|
|
302
|
+
string containing all equally represented bases in alphabetical order
|
|
303
|
+
</p>
|
|
304
|
+
</div>
|
|
305
|
+
</div>
|
|
306
|
+
|
|
307
|
+
<div id="method-M000003" class="method-detail">
|
|
308
|
+
<a name="M000003"></a>
|
|
309
|
+
|
|
310
|
+
<div class="method-heading">
|
|
311
|
+
<a href="Pileup.src/M000003.html" target="Code" class="method-signature"
|
|
312
|
+
onclick="popupCode('Pileup.src/M000003.html');return false;">
|
|
313
|
+
<span class="method-name">non_ref_count</span><span class="method-args">()</span>
|
|
314
|
+
</a>
|
|
315
|
+
</div>
|
|
316
|
+
|
|
317
|
+
<div class="method-description">
|
|
318
|
+
<p>
|
|
319
|
+
returns the total non-reference bases in the reads at this position
|
|
320
|
+
</p>
|
|
321
|
+
</div>
|
|
322
|
+
</div>
|
|
323
|
+
|
|
324
|
+
<div id="method-M000002" class="method-detail">
|
|
325
|
+
<a name="M000002"></a>
|
|
326
|
+
|
|
327
|
+
<div class="method-heading">
|
|
328
|
+
<a href="Pileup.src/M000002.html" target="Code" class="method-signature"
|
|
329
|
+
onclick="popupCode('Pileup.src/M000002.html');return false;">
|
|
330
|
+
<span class="method-name">non_refs</span><span class="method-args">()</span>
|
|
331
|
+
</a>
|
|
332
|
+
</div>
|
|
333
|
+
|
|
334
|
+
<div class="method-description">
|
|
335
|
+
<p>
|
|
336
|
+
Calculate the total count of each non-reference nucleotide and return a
|
|
337
|
+
hash of all 4 nt counts, returns a hash
|
|
338
|
+
</p>
|
|
339
|
+
<pre>
|
|
340
|
+
pile.non_refs #{:A => 1, :C => 0, :T => 0, :G => 0}
|
|
341
|
+
</pre>
|
|
342
|
+
</div>
|
|
343
|
+
</div>
|
|
344
|
+
|
|
345
|
+
<div id="method-M000004" class="method-detail">
|
|
346
|
+
<a name="M000004"></a>
|
|
347
|
+
|
|
348
|
+
<div class="method-heading">
|
|
349
|
+
<a href="Pileup.src/M000004.html" target="Code" class="method-signature"
|
|
350
|
+
onclick="popupCode('Pileup.src/M000004.html');return false;">
|
|
351
|
+
<span class="method-name">ref_count</span><span class="method-args">()</span>
|
|
352
|
+
</a>
|
|
353
|
+
</div>
|
|
354
|
+
|
|
355
|
+
<div class="method-description">
|
|
356
|
+
<p>
|
|
357
|
+
returns the count of reference-bases in the reads at this position
|
|
358
|
+
</p>
|
|
359
|
+
</div>
|
|
360
|
+
</div>
|
|
361
|
+
|
|
362
|
+
|
|
363
|
+
</div>
|
|
364
|
+
|
|
365
|
+
|
|
366
|
+
</div>
|
|
367
|
+
|
|
368
|
+
|
|
369
|
+
<div id="validator-badges">
|
|
370
|
+
<p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
|
|
371
|
+
</div>
|
|
372
|
+
|
|
373
|
+
</body>
|
|
374
|
+
</html>
|