bio-samtools 0.5.3 → 0.6.0

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Files changed (29) hide show
  1. data/VERSION +1 -1
  2. data/bio-samtools.gemspec +12 -15
  3. data/doc/Bio.html +7 -7
  4. data/doc/Bio/DB.html +2 -2
  5. data/doc/Bio/DB/Alignment.html +6 -6
  6. data/doc/Bio/DB/Pileup.html +190 -7
  7. data/doc/Bio/DB/SAM.html +58 -22
  8. data/doc/Bio/DB/SAM/Library.html +7 -7
  9. data/doc/Bio/DB/SAM/Tools.html +2 -2
  10. data/doc/Bio/DB/SAM/Tools/Bam1CoreT.html +2 -2
  11. data/doc/Bio/DB/SAM/Tools/Bam1T.html +2 -2
  12. data/doc/Bio/DB/SAM/Tools/BamHeaderT.html +2 -2
  13. data/doc/Bio/DB/SAM/Tools/BamPileup1T.html +2 -2
  14. data/doc/Bio/DB/SAM/Tools/SamfileT.html +2 -2
  15. data/doc/Bio/DB/SAM/Tools/SamfileTX.html +2 -2
  16. data/doc/Bio/DB/SAMException.html +3 -3
  17. data/doc/Bio/DB/Tag.html +3 -3
  18. data/doc/Bio/DB/Vcf.html +5 -5
  19. data/doc/LICENSE_txt.html +58 -55
  20. data/doc/LibC.html +2 -2
  21. data/doc/created.rid +7 -7
  22. data/doc/index.html +1 -1
  23. data/doc/js/search_index.js +1 -1
  24. data/doc/lib/bio/db/pileup_rb.html +5 -5
  25. data/doc/table_of_contents.html +19 -9
  26. data/lib/bio/db/pileup.rb +113 -3
  27. data/lib/bio/db/sam.rb +8 -2
  28. data/test/test_basic.rb +9 -0
  29. metadata +67 -22
data/VERSION CHANGED
@@ -1 +1 @@
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- 0.5.3
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+ 0.6.0
data/bio-samtools.gemspec CHANGED
@@ -4,18 +4,15 @@
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  # -*- encoding: utf-8 -*-
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  Gem::Specification.new do |s|
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- s.name = %q{bio-samtools}
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- s.version = "0.5.3"
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+ s.name = "bio-samtools"
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+ s.version = "0.6.0"
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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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- s.date = %q{2012-04-14}
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- s.description = %q{Binder of samtools for ruby, on the top of FFI.
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-
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- 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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- s.email = %q{ilpuccio.febo@gmail.com}
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- s.extensions = [%q{ext/mkrf_conf.rb}]
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+ s.authors = ["Ricardo Ramirez-Gonzalez", "Dan MacLean", "Raoul J.P. Bonnal"]
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+ s.date = "2012-12-03"
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+ s.description = "Binder of samtools for ruby, on the top of FFI. \n\n This project was born from the need to add support of BAM files to \n the gee_fu genome browser (http://github.com/danmaclean/gee_fu)."
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+ s.email = "ilpuccio.febo@gmail.com"
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+ s.extensions = ["ext/mkrf_conf.rb"]
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  s.extra_rdoc_files = [
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  "LICENSE.txt",
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  "README.rdoc"
@@ -194,11 +191,11 @@ Gem::Specification.new do |s|
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  "test/test_bio-samtools.rb",
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  "test/test_vcf.rb"
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  ]
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- s.homepage = %q{http://github.com/helios/bioruby-samtools}
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- s.licenses = [%q{MIT}]
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- s.require_paths = [%q{lib}]
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- s.rubygems_version = %q{1.8.6}
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- s.summary = %q{Binder of samtools for ruby, on the top of FFI.}
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+ s.homepage = "http://github.com/helios/bioruby-samtools"
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+ s.licenses = ["MIT"]
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+ s.require_paths = ["lib"]
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+ s.rubygems_version = "1.8.24"
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+ s.summary = "Binder of samtools for ruby, on the top of FFI."
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  if s.respond_to? :specification_version then
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  s.specification_version = 3
data/doc/Bio.html CHANGED
@@ -4,7 +4,7 @@
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  <head>
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- <title>Module: Bio</title>
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+ <title>module Bio - Pileup</title>
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@@ -178,13 +178,13 @@ the 1st indel allele otherwise</p>
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  <p>(13) indel line only: # reads supporting a third indel allele</p>
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  </li></ul>
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- <p>If pileup is invoked without `-c’, indel lines and columns between 3 and 7
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- inclusive will not be outputted.</p>
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+ <p>If pileup is invoked without `-c’, indel lines and columns between 3 and
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+ 7 inclusive will not be outputted.</p>
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  <p>NB mpileup uses the 6 column output format eg
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- “seq2t151tGtGt36t0t99t12t.….……At:9&lt;;;7=&lt;&lt;&lt;&lt;&lt;” Pileup
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- provides accessors for all columns (6 or 10 column format) and a few other
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- useful methods</p>
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+ “seq2t151tGtGt36t0t99t12t.….……At:9&lt;;;7=&lt;&lt;&lt;&lt;&lt;”
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+ Pileup provides accessors for all columns (6 or 10 column format) and a few
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+ other useful methods</p>
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  <p>require ‘rubygems’ require ‘ffi’</p>
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@@ -232,7 +232,7 @@ href="http://www.1000genomes.org/node/101">www.1000genomes.org/node/101</a></p>
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  <footer id="validator-badges">
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  <p><a href="http://validator.w3.org/check/referer">[Validate]</a>
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- <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 3.11.
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+ <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 3.12.
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  <p>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish Rdoc Generator</a> 3.
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  </footer>
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data/doc/Bio/DB.html CHANGED
@@ -4,7 +4,7 @@
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- <title>Class: Bio::DB</title>
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+ <title>class Bio::DB - Pileup</title>
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@@ -159,7 +159,7 @@
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  <p><a href="http://validator.w3.org/check/referer">[Validate]</a>
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- <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 3.11.
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+ <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 3.12.
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  <p>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish Rdoc Generator</a> 3.
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  </footer>
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data/doc/Bio/DB/Alignment.html CHANGED
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+ <title>class Bio::DB::Alignment - Pileup</title>
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@@ -595,7 +595,7 @@ for clarity. primary is the negation of is_negative from the BAM format</p>
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- <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 554</span>
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+ <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 560</span>
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  <span class="ruby-keyword">def</span> <span class="ruby-constant">Alignment</span>.<span class="ruby-identifier">finalize</span>(<span class="ruby-identifier">object_id</span>)
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  <span class="ruby-comment"># puts &quot;Object #{object_id} dying at #{Time.new}&quot;</span>
@@ -634,7 +634,7 @@ for clarity. primary is the negation of is_negative from the BAM format</p>
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- <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 550</span>
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+ <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 556</span>
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  <span class="ruby-keyword">def</span> <span class="ruby-identifier">initialize</span>
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  <span class="ruby-constant">ObjectSpace</span>.<span class="ruby-identifier">define_finalizer</span>(<span class="ruby-keyword">self</span>,
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  <span class="ruby-keyword">self</span>.<span class="ruby-identifier">class</span>.<span class="ruby-identifier">method</span>(<span class="ruby-value">:finalize</span>).<span class="ruby-identifier">to_proc</span>)
@@ -671,7 +671,7 @@ for clarity. primary is the negation of is_negative from the BAM format</p>
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  <div class="method-source-code" id="sam-3D-source">
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- <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 608</span>
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+ <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 614</span>
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  <span class="ruby-keyword">def</span> <span class="ruby-identifier">sam=</span>(<span class="ruby-identifier">sam</span>)
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  <span class="ruby-comment">#p sam</span>
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  <span class="ruby-identifier">s</span> = <span class="ruby-identifier">sam</span>.<span class="ruby-identifier">split</span>(<span class="ruby-string">&quot;\t&quot;</span>)
@@ -724,7 +724,7 @@ for clarity. primary is the negation of is_negative from the BAM format</p>
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- <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 576</span>
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+ <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 582</span>
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  <span class="ruby-keyword">def</span> <span class="ruby-identifier">set</span>(<span class="ruby-identifier">bam_alignment</span>, <span class="ruby-identifier">header</span>)
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  <span class="ruby-comment">#Create the FFI object</span>
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  <span class="ruby-ivar">@al</span> = <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-operator">::</span><span class="ruby-constant">Bam1T</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">bam_alignment</span>)
@@ -774,7 +774,7 @@ for clarity. primary is the negation of is_negative from the BAM format</p>
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- <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 3.11.
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+ <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 3.12.
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  <p>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish Rdoc Generator</a> 3.
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data/doc/Bio/DB/Pileup.html CHANGED
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@@ -70,14 +70,22 @@
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+ <li><a href="#method-c-iupac_to_base">::iupac_to_base</a>
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  <li><a href="#method-c-new">::new</a>
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+ <li><a href="#method-i-genotype_list">#genotype_list</a>
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+
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  <li><a href="#method-i-non_ref_count">#non_ref_count</a>
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  <li><a href="#method-i-ref_count">#ref_count</a>
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+ <li><a href="#method-i-to_s">#to_s</a>
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+ </div>
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+ </div>
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+ <div id="attribute-i-indel_1" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">indel_1</span><span
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@@ -342,6 +376,44 @@
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  <h3 class="section-header">Public Class Methods</h3>
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+ <div id="method-c-iupac_to_base" class="method-detail ">
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+ <span class="method-click-advice">click to toggle source</span>
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+ </div>
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+ <pre><span class="ruby-comment"># File lib/bio/db/pileup.rb, line 184</span>
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398
+ <span class="ruby-keyword">when</span> <span class="ruby-string">'K'</span> <span class="ruby-keyword">then</span> [<span class="ruby-string">'G'</span>,<span class="ruby-string">'T'</span>]
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+ <span class="ruby-keyword">when</span> <span class="ruby-string">'M'</span> <span class="ruby-keyword">then</span> [<span class="ruby-string">'A'</span>,<span class="ruby-string">'C'</span>]
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+ <span class="ruby-keyword">when</span> <span class="ruby-string">'S'</span> <span class="ruby-keyword">then</span> [<span class="ruby-string">'C'</span>,<span class="ruby-string">'G'</span>]
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+ <span class="ruby-keyword">when</span> <span class="ruby-string">'R'</span> <span class="ruby-keyword">then</span> [<span class="ruby-string">'A'</span>,<span class="ruby-string">'G'</span>]
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+ <span class="ruby-keyword">when</span> <span class="ruby-string">'W'</span> <span class="ruby-keyword">then</span> [<span class="ruby-string">'A'</span>,<span class="ruby-string">'T'</span>]
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+ <span class="ruby-keyword">when</span> <span class="ruby-string">'Y'</span> <span class="ruby-keyword">then</span> [<span class="ruby-string">'C'</span>,<span class="ruby-string">'T'</span>]
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@@ -363,11 +435,15 @@ pile = Bio::DB::Pileup.new(pile_up_line)</pre>
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  <pre><span class="ruby-comment"># File lib/bio/db/pileup.rb, line 35</span>
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  <span class="ruby-keyword">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">pile_up_line</span>)
366
- <span class="ruby-identifier">cols</span> = <span class="ruby-identifier">pile_up_line</span>.<span class="ruby-identifier">split</span>(<span class="ruby-regexp">/\t/</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">%r\t/</span>)
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  <span class="ruby-keyword">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">##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">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">##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-keyword">if</span> <span class="ruby-identifier">cols</span>[<span class="ruby-value">2</span>] <span class="ruby-operator">==</span> <span class="ruby-string">'*'</span> <span class="ruby-comment">#indel</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">@indel_1</span>, <span class="ruby-ivar">@indel_2</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>
444
+ <span class="ruby-keyword">else</span> <span class="ruby-comment">#snp / identity</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-identifier">cols</span>
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+ <span class="ruby-keyword">end</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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@@ -397,6 +473,40 @@ pile = Bio::DB::Pileup.new(pile_up_line)</pre>
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473
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398
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+ <div class="method-source-code" id="genotype_list-source">
492
+ <pre><span class="ruby-comment"># File lib/bio/db/pileup.rb, line 174</span>
493
+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">genotype_list</span>
494
+ <span class="ruby-keyword">if</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">ref_base</span> <span class="ruby-operator">==</span> <span class="ruby-string">'*'</span>
495
+ <span class="ruby-keyword">return</span> <span class="ruby-identifier">indel_gt</span>
496
+ <span class="ruby-keyword">else</span>
497
+ <span class="ruby-keyword">return</span> <span class="ruby-identifier">snp_gt</span>
498
+ <span class="ruby-keyword">end</span>
499
+ <span class="ruby-keyword">end</span></pre>
500
+ </div><!-- genotype_list-source -->
501
+
502
+ </div>
503
+
504
+
505
+
506
+
507
+ </div><!-- genotype_list-method -->
508
+
509
+
400
510
  <div id="method-i-non_ref_count" class="method-detail ">
401
511
 
402
512
  <div class="method-heading">
@@ -413,7 +523,7 @@ pile = Bio::DB::Pileup.new(pile_up_line)</pre>
413
523
 
414
524
 
415
525
  <div class="method-source-code" id="non_ref_count-source">
416
- <pre><span class="ruby-comment"># File lib/bio/db/pileup.rb, line 65</span>
526
+ <pre><span class="ruby-comment"># File lib/bio/db/pileup.rb, line 69</span>
417
527
  <span class="ruby-keyword">def</span> <span class="ruby-identifier">non_ref_count</span>
418
528
  <span class="ruby-keyword">if</span> <span class="ruby-ivar">@non_ref_count</span>.<span class="ruby-identifier">nil?</span>
419
529
  <span class="ruby-ivar">@non_ref_count</span> = <span class="ruby-ivar">@read_bases</span>.<span class="ruby-identifier">count</span>(<span class="ruby-string">&quot;ATGCatgc&quot;</span>).<span class="ruby-identifier">to_f</span>
@@ -450,7 +560,7 @@ hash of all 4 nt counts, returns a hash</p>
450
560
 
451
561
 
452
562
  <div class="method-source-code" id="non_refs-source">
453
- <pre><span class="ruby-comment"># File lib/bio/db/pileup.rb, line 57</span>
563
+ <pre><span class="ruby-comment"># File lib/bio/db/pileup.rb, line 61</span>
454
564
  <span class="ruby-keyword">def</span> <span class="ruby-identifier">non_refs</span>
455
565
  <span class="ruby-keyword">if</span> <span class="ruby-ivar">@non_ref_count_hash</span>.<span class="ruby-identifier">nil?</span>
456
566
  <span class="ruby-ivar">@non_ref_count_hash</span> = {<span class="ruby-value">:A</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">read_bases</span>.<span class="ruby-identifier">count</span>(<span class="ruby-string">&quot;Aa&quot;</span>), <span class="ruby-value">:C</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">read_bases</span>.<span class="ruby-identifier">count</span>(<span class="ruby-string">&quot;Cc&quot;</span>), <span class="ruby-value">:G</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">read_bases</span>.<span class="ruby-identifier">count</span>(<span class="ruby-string">&quot;Gg&quot;</span>), <span class="ruby-value">:T</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">read_bases</span>.<span class="ruby-identifier">count</span>(<span class="ruby-string">&quot;Tt&quot;</span>)}
@@ -483,7 +593,7 @@ hash of all 4 nt counts, returns a hash</p>
483
593
 
484
594
 
485
595
  <div class="method-source-code" id="ref_count-source">
486
- <pre><span class="ruby-comment"># File lib/bio/db/pileup.rb, line 73</span>
596
+ <pre><span class="ruby-comment"># File lib/bio/db/pileup.rb, line 77</span>
487
597
  <span class="ruby-keyword">def</span> <span class="ruby-identifier">ref_count</span>
488
598
  <span class="ruby-keyword">if</span> <span class="ruby-ivar">@ref_count</span>.<span class="ruby-identifier">nil?</span>
489
599
  <span class="ruby-ivar">@ref_count</span> = <span class="ruby-keyword">self</span>.<span class="ruby-identifier">read_bases</span>.<span class="ruby-identifier">count</span>(<span class="ruby-string">&quot;.,&quot;</span>)
@@ -500,6 +610,79 @@ hash of all 4 nt counts, returns a hash</p>
500
610
  </div><!-- ref_count-method -->
501
611
 
502
612
 
613
+ <div id="method-i-to_s" class="method-detail ">
614
+
615
+ <div class="method-heading">
616
+ <span class="method-name">to_s</span><span
617
+ class="method-args">()</span>
618
+ <span class="method-click-advice">click to toggle source</span>
619
+ </div>
620
+
621
+
622
+ <div class="method-description">
623
+
624
+ <p>returns pileup format line as</p>
625
+
626
+
627
+
628
+ <div class="method-source-code" id="to_s-source">
629
+ <pre><span class="ruby-comment"># File lib/bio/db/pileup.rb, line 197</span>
630
+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">to_s</span>
631
+ <span class="ruby-keyword">if</span> <span class="ruby-ivar">@read_quals</span> <span class="ruby-keyword">and</span> <span class="ruby-operator">!</span><span class="ruby-ivar">@consensus_quality</span> <span class="ruby-comment">#6col</span>
632
+ [<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-identifier">to_i</span>, <span class="ruby-ivar">@read_bases</span>, <span class="ruby-ivar">@read_quals</span>].<span class="ruby-identifier">join</span>(<span class="ruby-string">&quot;\t&quot;</span>)
633
+ <span class="ruby-keyword">elsif</span> <span class="ruby-ivar">@indel_1</span> <span class="ruby-comment">#13 cols</span>
634
+ [<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-identifier">to_i</span>, <span class="ruby-ivar">@snp_quality</span>.<span class="ruby-identifier">to_i</span>, <span class="ruby-ivar">@rms_mapq</span>.<span class="ruby-identifier">to_i</span>, <span class="ruby-ivar">@coverage</span>.<span class="ruby-identifier">to_i</span>, <span class="ruby-ivar">@indel_1</span>, <span class="ruby-ivar">@indel_2</span>, <span class="ruby-ivar">@ar1</span>, <span class="ruby-ivar">@ar2</span>, <span class="ruby-ivar">@ar3</span>].<span class="ruby-identifier">join</span>(<span class="ruby-string">&quot;\t&quot;</span>)
635
+ <span class="ruby-keyword">else</span> <span class="ruby-comment">#10 cols</span>
636
+ [<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-identifier">to_i</span>, <span class="ruby-ivar">@snp_quality</span>.<span class="ruby-identifier">to_i</span>, <span class="ruby-ivar">@rms_mapq</span>.<span class="ruby-identifier">to_i</span>, <span class="ruby-ivar">@coverage</span>.<span class="ruby-identifier">to_i</span>, <span class="ruby-ivar">@read_bases</span>, <span class="ruby-ivar">@read_quals</span>].<span class="ruby-identifier">join</span>(<span class="ruby-string">&quot;\t&quot;</span>)
637
+ <span class="ruby-keyword">end</span>
638
+
639
+ <span class="ruby-keyword">end</span></pre>
640
+ </div><!-- to_s-source -->
641
+
642
+ </div>
643
+
644
+
645
+
646
+
647
+ </div><!-- to_s-method -->
648
+
649
+
650
+ <div id="method-i-to_vcf" class="method-detail ">
651
+
652
+ <div class="method-heading">
653
+ <span class="method-name">to_vcf</span><span
654
+ class="method-args">()</span>
655
+ <span class="method-click-advice">click to toggle source</span>
656
+ </div>
657
+
658
+
659
+ <div class="method-description">
660
+
661
+ <p>returns basic VCF string as per samtools/misc sam2vcf.pl except that it
662
+ scrimps on the ref for indels, returning a ‘*’ instead of the reference
663
+ allele</p>
664
+
665
+
666
+
667
+ <div class="method-source-code" id="to_vcf-source">
668
+ <pre><span class="ruby-comment"># File lib/bio/db/pileup.rb, line 103</span>
669
+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">to_vcf</span>
670
+
671
+ <span class="ruby-identifier">alt</span>,<span class="ruby-identifier">g</span> = <span class="ruby-keyword">self</span>.<span class="ruby-identifier">genotype_list</span>
672
+ <span class="ruby-identifier">alt</span> = <span class="ruby-keyword">self</span>.<span class="ruby-identifier">consensus</span>.<span class="ruby-identifier">split</span>(<span class="ruby-regexp">%r/</span>).<span class="ruby-identifier">join</span>(<span class="ruby-string">','</span>) <span class="ruby-keyword">unless</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">ref_base</span> <span class="ruby-operator">==</span> <span class="ruby-string">'*'</span>
673
+ <span class="ruby-identifier">alt</span> = <span class="ruby-string">'.'</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">alt</span> <span class="ruby-operator">==</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">ref_base</span>
674
+ [<span class="ruby-keyword">self</span>.<span class="ruby-identifier">ref_name</span>, <span class="ruby-keyword">self</span>.<span class="ruby-identifier">pos</span>, <span class="ruby-string">'.'</span>, <span class="ruby-keyword">self</span>.<span class="ruby-identifier">ref_base</span>, <span class="ruby-identifier">alt</span>, <span class="ruby-keyword">self</span>.<span class="ruby-identifier">snp_quality</span>.<span class="ruby-identifier">to_i</span>, <span class="ruby-string">&quot;0&quot;</span>, <span class="ruby-node">&quot;DP=#{self.coverage.to_i}&quot;</span>, <span class="ruby-string">&quot;GT:GQ:DP&quot;</span>, <span class="ruby-node">&quot;#{g}:#{self.consensus_quality.to_i}:#{self.coverage.to_i}&quot;</span> ].<span class="ruby-identifier">join</span>(<span class="ruby-string">&quot;\t&quot;</span>)
675
+ <span class="ruby-keyword">end</span></pre>
676
+ </div><!-- to_vcf-source -->
677
+
678
+ </div>
679
+
680
+
681
+
682
+
683
+ </div><!-- to_vcf-method -->
684
+
685
+
503
686
  </section><!-- public-instance-method-details -->
504
687
 
505
688
  </section><!-- 5Buntitled-5D -->
@@ -509,7 +692,7 @@ hash of all 4 nt counts, returns a hash</p>
509
692
 
510
693
  <footer id="validator-badges">
511
694
  <p><a href="http://validator.w3.org/check/referer">[Validate]</a>
512
- <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 3.11.
695
+ <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 3.12.
513
696
  <p>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish Rdoc Generator</a> 3.
514
697
  </footer>
515
698
 
data/doc/Bio/DB/SAM.html CHANGED
@@ -4,7 +4,7 @@
4
4
  <head>
5
5
  <meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
6
6
 
7
- <title>Class: Bio::DB::Sam</title>
7
+ <title>class Bio::DB::Sam - Pileup</title>
8
8
 
9
9
  <link type="text/css" media="screen" href="../../rdoc.css" rel="stylesheet">
10
10
 
@@ -84,6 +84,8 @@
84
84
 
85
85
  <li><a href="#method-i-deprecated_pileup">#deprecated_pileup</a>
86
86
 
87
+ <li><a href="#method-i-each_reference">#each_reference</a>
88
+
87
89
  <li><a href="#method-i-fetch">#fetch</a>
88
90
 
89
91
  <li><a href="#method-i-fetch_reference">#fetch_reference</a>
@@ -337,10 +339,10 @@ following elemets:</p>
337
339
  <p>If the file is to be writen (false). Not supported yet.</p>
338
340
  </dd></dl>
339
341
 
340
- <p><strong>NOTE:</strong> you can't use binary and text formats simultaneusly.
341
- To make queries, the file has to be a sorted binary. This function doesn't
342
- actually open the file, it just prepares the object to be opened in a later
343
- stage.</p>
342
+ <p><strong>NOTE:</strong> you can’t use binary and text formats
343
+ simultaneusly. To make queries, the file has to be a sorted binary. This
344
+ function doesn’t actually open the file, it just prepares the object to
345
+ be opened in a later stage.</p>
344
346
 
345
347
 
346
348
 
@@ -542,8 +544,8 @@ method you must have a version of samtools that supports the pileup command
542
544
  (&lt; 0.1.17) otherwise the command will fail. mpileup is the preferred
543
545
  method for getting pileups. With this method the sam object should be
544
546
  created as usual, but you need to pass this method a string of options for
545
- samtools you don’t need to provide the call to samtools pileup itself or -f
546
- &lt;fasta file&gt; or the bam file itself, these are taken from the sam
547
+ samtools you don’t need to provide the call to samtools pileup itself or
548
+ -f &lt;fasta file&gt; or the bam file itself, these are taken from the sam
547
549
  object</p>
548
550
 
549
551
 
@@ -579,6 +581,39 @@ object</p>
579
581
  </div><!-- deprecated_pileup-method -->
580
582
 
581
583
 
584
+ <div id="method-i-each_reference" class="method-detail ">
585
+
586
+ <div class="method-heading">
587
+ <span class="method-name">each_reference</span><span
588
+ class="method-args">() { |k, v| ... }</span>
589
+ <span class="method-click-advice">click to toggle source</span>
590
+ </div>
591
+
592
+
593
+ <div class="method-description">
594
+
595
+ <p>yields each reference name and its length</p>
596
+
597
+
598
+
599
+ <div class="method-source-code" id="each_reference-source">
600
+ <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 535</span>
601
+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">each_reference</span>
602
+ <span class="ruby-identifier">refs</span> = <span class="ruby-identifier">index_stats</span>
603
+ <span class="ruby-identifier">refs</span>.<span class="ruby-identifier">each_pair</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">k</span>, <span class="ruby-identifier">v</span><span class="ruby-operator">|</span>
604
+ <span class="ruby-keyword">yield</span> <span class="ruby-identifier">k</span>, <span class="ruby-identifier">v</span>[<span class="ruby-value">:length</span>]
605
+ <span class="ruby-keyword">end</span>
606
+ <span class="ruby-keyword">end</span></pre>
607
+ </div><!-- each_reference-source -->
608
+
609
+ </div>
610
+
611
+
612
+
613
+
614
+ </div><!-- each_reference-method -->
615
+
616
+
582
617
  <div id="method-i-fetch" class="method-detail ">
583
618
 
584
619
  <div class="method-heading">
@@ -755,7 +790,7 @@ use your own FixNum (FFI-bug?)</p>
755
790
  <span class="ruby-keyword">begin</span>
756
791
 
757
792
  <span class="ruby-keyword">while</span> <span class="ruby-identifier">line</span> = <span class="ruby-identifier">read_pipe</span>.<span class="ruby-identifier">readline</span> <span class="ruby-comment">#TAB delimited with each line consisting of reference sequence name, sequence length, # mapped reads and # unmapped reads.</span>
758
- <span class="ruby-identifier">info</span> = <span class="ruby-identifier">line</span>.<span class="ruby-identifier">split</span>(<span class="ruby-regexp">/\t/</span>)
793
+ <span class="ruby-identifier">info</span> = <span class="ruby-identifier">line</span>.<span class="ruby-identifier">split</span>(<span class="ruby-regexp">%r\t/</span>)
759
794
  <span class="ruby-keyword">next</span> <span class="ruby-keyword">unless</span> <span class="ruby-identifier">info</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">==</span> <span class="ruby-value">4</span>
760
795
  <span class="ruby-identifier">index_stats</span>[ <span class="ruby-identifier">info</span>[<span class="ruby-value">0</span>] ] = {<span class="ruby-value">:length</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">info</span>[<span class="ruby-value">1</span>].<span class="ruby-identifier">to_i</span>, <span class="ruby-value">:mapped_reads</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">info</span>[<span class="ruby-value">2</span>].<span class="ruby-identifier">to_i</span>, <span class="ruby-value">:unmapped_reads</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">info</span>[<span class="ruby-value">3</span>].<span class="ruby-identifier">to_i</span> }
761
796
  <span class="ruby-keyword">end</span>
@@ -790,10 +825,10 @@ use your own FixNum (FFI-bug?)</p>
790
825
  <p>Loads the bam index to be used for fetching. If the index doesn’t exists
791
826
  the index is built provided that the user has writing access to the folder
792
827
  where the BAM file is located. If the creation of the file fails a <a
793
- href="SAMException.html">SAMException</a> is thrown. If the index doesn’t
794
- exist, loading it will take more time. It is suggested to generate the
795
- index separatedly if the bam file sits on a server where the executing user
796
- may not have writing permissions in the server.</p>
828
+ href="SAMException.html">SAMException</a> is thrown. If the index
829
+ doesn’t exist, loading it will take more time. It is suggested to
830
+ generate the index separatedly if the bam file sits on a server where the
831
+ executing user may not have writing permissions in the server.</p>
797
832
 
798
833
 
799
834
 
@@ -831,10 +866,11 @@ may not have writing permissions in the server.</p>
831
866
  <div class="method-description">
832
867
 
833
868
  <p>Loads the reference file to be able to query regions of it. This requires
834
- the fai index to exist in the same folder than the reference. If it doesn’t
835
- exisits, this functions attempts to generate it. If user doesn’t have
836
- writing permissions on the folder, or the creation of the fai fails for any
837
- reason, a <a href="SAMException.html">SAMException</a> is thrown.</p>
869
+ the fai index to exist in the same folder than the reference. If it
870
+ doesn’t exisits, this functions attempts to generate it. If user
871
+ doesn’t have writing permissions on the folder, or the creation of the
872
+ fai fails for any reason, a <a href="SAMException.html">SAMException</a> is
873
+ thrown.</p>
838
874
 
839
875
 
840
876
 
@@ -867,7 +903,7 @@ reason, a <a href="SAMException.html">SAMException</a> is thrown.</p>
867
903
 
868
904
  <div class="method-heading">
869
905
  <span class="method-name">mpileup</span><span
870
- class="method-args">( opts ) { |pileup| ... }</span>
906
+ class="method-args">( opts={}) { |pileup| ... }</span>
871
907
  <span class="method-click-advice">click to toggle source</span>
872
908
  </div>
873
909
 
@@ -879,15 +915,15 @@ command line options for mpileup. is an iterator that yields a <a
879
915
  href="Pileup.html">Pileup</a> object for each postion the command line
880
916
  options that generate/affect BCF/VCF are ignored ie (g,u,e,h,I,L,o,p) call
881
917
  the option as a symbol of the flag, eg -r for region is called :r =&gt;
882
- “some <a href="SAM.html">SAM</a> compatible region” eg bam.mpileup(:r =&gt;
883
- “chr1:1000-2000”, :q =&gt; 50) gets the bases with quality &gt; 50 on chr1
884
- between 1000-5000</p>
918
+ “some <a href="SAM.html">SAM</a> compatible region” eg bam.mpileup(:r
919
+ =&gt; “chr1:1000-2000”, :q =&gt; 50) gets the bases with quality &gt;
920
+ 50 on chr1 between 1000-5000</p>
885
921
 
886
922
 
887
923
 
888
924
  <div class="method-source-code" id="mpileup-source">
889
925
  <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 281</span>
890
- <span class="ruby-keyword">def</span> <span class="ruby-identifier">mpileup</span>( <span class="ruby-identifier">opts</span> )
926
+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">mpileup</span>( <span class="ruby-identifier">opts</span>={})
891
927
 
892
928
  <span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-string">&quot;No BAMFile provided&quot;</span> <span class="ruby-keyword">unless</span> <span class="ruby-ivar">@sam</span> <span class="ruby-keyword">and</span> <span class="ruby-ivar">@binary</span>
893
929
  <span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-string">&quot;No FastA provided&quot;</span> <span class="ruby-keyword">unless</span> <span class="ruby-ivar">@fasta_path</span>
@@ -1235,7 +1271,7 @@ binary or text, the path and the fasta file of the reference</p>
1235
1271
 
1236
1272
  <footer id="validator-badges">
1237
1273
  <p><a href="http://validator.w3.org/check/referer">[Validate]</a>
1238
- <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 3.11.
1274
+ <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 3.12.
1239
1275
  <p>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish Rdoc Generator</a> 3.
1240
1276
  </footer>
1241
1277