bio-samtools 0.4.2 → 0.5.0

data/doc/Bio/DB/SAM.html

@@ -133,6 +133,8 @@
   
     <li><a href="../../Bio/DB/Alignment.html">Bio::DB::Alignment</a>
   
+    <li><a href="../../Bio/DB/Pileup.html">Bio::DB::Pileup</a>
+  
     <li><a href="../../Bio/DB/SAM.html">Bio::DB::SAM</a>
   
     <li><a href="../../Bio/DB/SAM/Library.html">Bio::DB::SAM::Library</a>
@@ -157,11 +159,9 @@
   
     <li><a href="../../Bio/DB/Tag.html">Bio::DB::Tag</a>
   
-    <li><a href="../../LibC.html">LibC</a>
-  
-    <li><a href="../../Pileup.html">Pileup</a>
+    <li><a href="../../Bio/DB/Vcf.html">Bio::DB::Vcf</a>
   
-    <li><a href="../../Vcf.html">Vcf</a>
+    <li><a href="../../LibC.html">LibC</a>
   
   </ul>
 </nav>
@@ -337,10 +337,10 @@ following elemets:</p>
 <p>If the file is to be writen (false). Not supported yet.</p>
 </dd></dl>
 
-<p><strong>NOTE:</strong> you can’t use binary and text formats
-simultaneusly. To make queries, the file has to be a sorted binary.  This
-function doesn’t actually open the file, it just prepares the object to
-be opened in a later stage.</p>
+<p><strong>NOTE:</strong> you can't use binary and text formats simultaneusly.
+To make queries, the file has to be a sorted binary.  This function doesn't
+actually open the file, it just prepares the object to be opened in a later
+stage.</p>
           
 
           
@@ -542,14 +542,14 @@ method you must have a version of samtools that supports the pileup command
 (&lt; 0.1.17) otherwise the command will fail. mpileup is the preferred
 method for getting pileups.  With this method the sam object should be
 created as usual, but you need to pass this method a string of options for
-samtools you don’t need to provide the call to samtools pileup itself or
--f &lt;fasta file&gt; or the bam file itself, these are taken from the sam
+samtools you don’t need to provide the call to samtools pileup itself or -f
+&lt;fasta file&gt; or the bam file itself, these are taken from the sam
 object</p>
           
 
           
           <div class="method-source-code" id="deprecated_pileup-source">
-            <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 472</span>
+            <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 473</span>
 <span class="ruby-keyword">def</span> <span class="ruby-identifier">deprecated_pileup</span>( <span class="ruby-identifier">cmd</span> )
   
   <span class="ruby-identifier">system</span>(<span class="ruby-string">'samtools pileup &gt; /dev/null 2&gt;&amp;1'</span>)
@@ -726,7 +726,7 @@ use your own FixNum (FFI-bug?)</p>
 
           
           <div class="method-source-code" id="index_stats-source">
-            <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 493</span>
+            <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 494</span>
 <span class="ruby-keyword">def</span> <span class="ruby-identifier">index_stats</span> 
   <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>
   <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>
@@ -790,10 +790,10 @@ use your own FixNum (FFI-bug?)</p>
           <p>Loads the bam index to be used for fetching. If the index doesn’t exists
 the index is built provided that the user has writing access to the folder
 where the BAM file is located. If the creation of the file fails a <a
-href="SAMException.html">SAMException</a> is thrown.  If the index
-doesn’t exist, loading it will take more time. It is suggested to
-generate the index separatedly if the bam file sits on a server where the
-executing user may not have writing permissions in the server.</p>
+href="SAMException.html">SAMException</a> is thrown.  If the index doesn’t
+exist, loading it will take more time. It is suggested to generate the
+index separatedly if the bam file sits on a server where the executing user
+may not have writing permissions in the server.</p>
           
 
           
@@ -831,11 +831,10 @@ executing user may not have writing permissions in the server.</p>
         <div class="method-description">
           
           <p>Loads the reference file to be able to query regions of it. This requires
-the fai index to exist in the same folder than the reference. If it
-doesn’t exisits, this functions attempts to generate it. If user
-doesn’t have writing permissions on the folder, or the creation of the
-fai fails for any reason, a <a href="SAMException.html">SAMException</a> is
-thrown.</p>
+the fai index to exist in the same folder than the reference. If it doesn’t
+exisits, this functions attempts to generate it. If user doesn’t have
+writing permissions on the folder, or the creation of the fai fails for any
+reason, a <a href="SAMException.html">SAMException</a> is thrown.</p>
           
 
           
@@ -877,12 +876,12 @@ thrown.</p>
           
           <p>calls the mpileup function, opts is a hash of options identical to the
 command line options for mpileup. is an iterator that yields a <a
-href="../../Pileup.html">Pileup</a> object for each postion the command
-line options that generate/affect BCF/VCF are ignored ie (g,u,e,h,I,L,o,p)
-call the option as a symbol of the flag, eg -r for region is called :r
-=&gt; “some <a href="SAM.html">SAM</a> compatible region” eg
-bam.mpileup(:r =&gt; “chr1:1000-2000”, :q =&gt; 50) gets the bases with
-quality &gt; 50 on chr1 between 1000-5000</p>
+href="Pileup.html">Pileup</a> object for each postion the command line
+options that generate/affect BCF/VCF are ignored ie (g,u,e,h,I,L,o,p) call
+the option as a symbol of the flag, eg -r for region is called :r =&gt;
+“some <a href="SAM.html">SAM</a> compatible region” eg bam.mpileup(:r =&gt;
+“chr1:1000-2000”, :q =&gt; 50) gets the bases with quality &gt; 50 on chr1
+between 1000-5000</p>
           
 
           
@@ -908,15 +907,15 @@ quality &gt; 50 on chr1 between 1000-5000</p>
         <span class="ruby-value">:min_mapping_quality</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:q</span>,
         <span class="ruby-value">:min_base_quality</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:Q</span>
         }
-
         <span class="ruby-comment">##convert any long_opts to short opts </span>
+        <span class="ruby-identifier">temp_opts</span> = <span class="ruby-identifier">opts</span>.<span class="ruby-identifier">dup</span>
         <span class="ruby-identifier">opts</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>
           <span class="ruby-keyword">if</span> <span class="ruby-identifier">long_opts</span>[<span class="ruby-identifier">k</span>]
-            <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> 
-            <span class="ruby-identifier">opts</span>.<span class="ruby-identifier">delete</span>(<span class="ruby-identifier">k</span>)
+            <span class="ruby-identifier">temp_opts</span>[<span class="ruby-identifier">long_opts</span>[<span class="ruby-identifier">k</span>]] = <span class="ruby-identifier">v</span> 
+            <span class="ruby-identifier">temp_opts</span>.<span class="ruby-identifier">delete</span>(<span class="ruby-identifier">k</span>)
           <span class="ruby-keyword">end</span>
         <span class="ruby-keyword">end</span>
-
+        <span class="ruby-identifier">opts</span> = <span class="ruby-identifier">temp_opts</span>
         <span class="ruby-comment">##remove any calls to -g or -u for mpileup, bcf output is not yet supported</span>
         <span class="ruby-comment">##and also associated output options</span>
         [<span class="ruby-value">:g</span>, <span class="ruby-value">:u</span>, <span class="ruby-value">:e</span>, <span class="ruby-value">:h</span>, <span class="ruby-value">:I</span>, <span class="ruby-value">:L</span>, <span class="ruby-value">:o</span>, <span class="ruby-value">: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>) }
@@ -935,7 +934,7 @@ quality &gt; 50 on chr1 between 1000-5000</p>
 
         <span class="ruby-identifier">sam_pipe</span> = <span class="ruby-constant">IO</span>.<span class="ruby-identifier">popen</span>(<span class="ruby-identifier">sam_command</span>)
         <span class="ruby-keyword">while</span> <span class="ruby-identifier">line</span> = <span class="ruby-identifier">sam_pipe</span>.<span class="ruby-identifier">gets</span>
-          <span class="ruby-keyword">yield</span> <span class="ruby-constant">Pileup</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">line</span>)
+          <span class="ruby-keyword">yield</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">Pileup</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">line</span>)
         <span class="ruby-keyword">end</span>
         <span class="ruby-identifier">sam_pipe</span>.<span class="ruby-identifier">close</span>
         <span class="ruby-comment">#strptrs &lt;&lt; FFI::MemoryPointer.from_string('-f')</span>
@@ -1028,13 +1027,14 @@ and supports returning of pileup vcf</p>
         }
 
         <span class="ruby-comment">##convert any long_opts to short opts </span>
+        <span class="ruby-identifier">temp_opts</span> = <span class="ruby-identifier">opts</span>.<span class="ruby-identifier">dup</span>
         <span class="ruby-identifier">opts</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>
           <span class="ruby-keyword">if</span> <span class="ruby-identifier">long_opts</span>[<span class="ruby-identifier">k</span>]
-            <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> 
-            <span class="ruby-identifier">opts</span>.<span class="ruby-identifier">delete</span>(<span class="ruby-identifier">k</span>)
+            <span class="ruby-identifier">temp_opts</span>[<span class="ruby-identifier">long_opts</span>[<span class="ruby-identifier">k</span>]] = <span class="ruby-identifier">v</span> 
+            <span class="ruby-identifier">temp_opts</span>.<span class="ruby-identifier">delete</span>(<span class="ruby-identifier">k</span>)
           <span class="ruby-keyword">end</span>
         <span class="ruby-keyword">end</span>
-
+        <span class="ruby-identifier">opts</span> = <span class="ruby-identifier">temp_opts</span>
         <span class="ruby-comment">##remove any calls to -g or -u for mpileup, bcf output is not yet supported</span>
         <span class="ruby-comment">##and also associated output options</span>
         <span class="ruby-comment">#[:g, :u, :e, :h, :I, :L, :o, :p].each {|x| opts.delete(x) }</span>
@@ -1061,11 +1061,11 @@ and supports returning of pileup vcf</p>
         <span class="ruby-keyword">if</span> <span class="ruby-identifier">opts</span>[<span class="ruby-value">:u</span>]
           <span class="ruby-keyword">while</span> <span class="ruby-identifier">line</span> = <span class="ruby-identifier">pipe</span>.<span class="ruby-identifier">gets</span>
             <span class="ruby-keyword">next</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">line</span>[<span class="ruby-value">0</span>,<span class="ruby-value">1</span>] <span class="ruby-operator">==</span> <span class="ruby-string">'#'</span> <span class="ruby-comment">#skip any header or meta-lines, we dont do anything with those </span>
-            <span class="ruby-keyword">yield</span> <span class="ruby-constant">Vcf</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">line</span>) 
+            <span class="ruby-keyword">yield</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">Vcf</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">line</span>) 
           <span class="ruby-keyword">end</span>
         <span class="ruby-keyword">else</span>
           <span class="ruby-keyword">while</span> <span class="ruby-identifier">line</span> = <span class="ruby-identifier">pipe</span>.<span class="ruby-identifier">gets</span>
-            <span class="ruby-keyword">yield</span> <span class="ruby-constant">Pileup</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">line</span>)
+            <span class="ruby-keyword">yield</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">Pileup</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">line</span>)
           <span class="ruby-keyword">end</span>
         <span class="ruby-keyword">end</span>
         <span class="ruby-identifier">pipe</span>.<span class="ruby-identifier">close</span>

data/doc/Bio/DB/SAM/Library.html

@@ -93,6 +93,8 @@
   
     <li><a href="../../../Bio/DB/Alignment.html">Bio::DB::Alignment</a>
   
+    <li><a href="../../../Bio/DB/Pileup.html">Bio::DB::Pileup</a>
+  
     <li><a href="../../../Bio/DB/SAM.html">Bio::DB::SAM</a>
   
     <li><a href="../../../Bio/DB/SAM/Library.html">Bio::DB::SAM::Library</a>
@@ -117,11 +119,9 @@
   
     <li><a href="../../../Bio/DB/Tag.html">Bio::DB::Tag</a>
   
-    <li><a href="../../../LibC.html">LibC</a>
-  
-    <li><a href="../../../Pileup.html">Pileup</a>
+    <li><a href="../../../Bio/DB/Vcf.html">Bio::DB::Vcf</a>
   
-    <li><a href="../../../Vcf.html">Vcf</a>
+    <li><a href="../../../LibC.html">LibC</a>
   
   </ul>
 </nav>

data/doc/Bio/DB/SAM/Tools.html

@@ -95,6 +95,8 @@
   
     <li><a href="../../../Bio/DB/Alignment.html">Bio::DB::Alignment</a>
   
+    <li><a href="../../../Bio/DB/Pileup.html">Bio::DB::Pileup</a>
+  
     <li><a href="../../../Bio/DB/SAM.html">Bio::DB::SAM</a>
   
     <li><a href="../../../Bio/DB/SAM/Library.html">Bio::DB::SAM::Library</a>
@@ -119,11 +121,9 @@
   
     <li><a href="../../../Bio/DB/Tag.html">Bio::DB::Tag</a>
   
-    <li><a href="../../../LibC.html">LibC</a>
-  
-    <li><a href="../../../Pileup.html">Pileup</a>
+    <li><a href="../../../Bio/DB/Vcf.html">Bio::DB::Vcf</a>
   
-    <li><a href="../../../Vcf.html">Vcf</a>
+    <li><a href="../../../LibC.html">LibC</a>
   
   </ul>
 </nav>

data/doc/Bio/DB/SAM/Tools/Bam1CoreT.html

@@ -89,6 +89,8 @@
   
     <li><a href="../../../../Bio/DB/Alignment.html">Bio::DB::Alignment</a>
   
+    <li><a href="../../../../Bio/DB/Pileup.html">Bio::DB::Pileup</a>
+  
     <li><a href="../../../../Bio/DB/SAM.html">Bio::DB::SAM</a>
   
     <li><a href="../../../../Bio/DB/SAM/Library.html">Bio::DB::SAM::Library</a>
@@ -113,11 +115,9 @@
   
     <li><a href="../../../../Bio/DB/Tag.html">Bio::DB::Tag</a>
   
-    <li><a href="../../../../LibC.html">LibC</a>
-  
-    <li><a href="../../../../Pileup.html">Pileup</a>
+    <li><a href="../../../../Bio/DB/Vcf.html">Bio::DB::Vcf</a>
   
-    <li><a href="../../../../Vcf.html">Vcf</a>
+    <li><a href="../../../../LibC.html">LibC</a>
   
   </ul>
 </nav>

data/doc/Bio/DB/SAM/Tools/Bam1T.html

@@ -99,6 +99,8 @@
   
     <li><a href="../../../../Bio/DB/Alignment.html">Bio::DB::Alignment</a>
   
+    <li><a href="../../../../Bio/DB/Pileup.html">Bio::DB::Pileup</a>
+  
     <li><a href="../../../../Bio/DB/SAM.html">Bio::DB::SAM</a>
   
     <li><a href="../../../../Bio/DB/SAM/Library.html">Bio::DB::SAM::Library</a>
@@ -123,11 +125,9 @@
   
     <li><a href="../../../../Bio/DB/Tag.html">Bio::DB::Tag</a>
   
-    <li><a href="../../../../LibC.html">LibC</a>
-  
-    <li><a href="../../../../Pileup.html">Pileup</a>
+    <li><a href="../../../../Bio/DB/Vcf.html">Bio::DB::Vcf</a>
   
-    <li><a href="../../../../Vcf.html">Vcf</a>
+    <li><a href="../../../../LibC.html">LibC</a>
   
   </ul>
 </nav>

data/doc/Bio/DB/SAM/Tools/BamHeaderT.html

@@ -101,6 +101,8 @@
   
     <li><a href="../../../../Bio/DB/Alignment.html">Bio::DB::Alignment</a>
   
+    <li><a href="../../../../Bio/DB/Pileup.html">Bio::DB::Pileup</a>
+  
     <li><a href="../../../../Bio/DB/SAM.html">Bio::DB::SAM</a>
   
     <li><a href="../../../../Bio/DB/SAM/Library.html">Bio::DB::SAM::Library</a>
@@ -125,11 +127,9 @@
   
     <li><a href="../../../../Bio/DB/Tag.html">Bio::DB::Tag</a>
   
-    <li><a href="../../../../LibC.html">LibC</a>
-  
-    <li><a href="../../../../Pileup.html">Pileup</a>
+    <li><a href="../../../../Bio/DB/Vcf.html">Bio::DB::Vcf</a>
   
-    <li><a href="../../../../Vcf.html">Vcf</a>
+    <li><a href="../../../../LibC.html">LibC</a>
   
   </ul>
 </nav>

data/doc/Bio/DB/SAM/Tools/BamPileup1T.html

@@ -89,6 +89,8 @@
   
     <li><a href="../../../../Bio/DB/Alignment.html">Bio::DB::Alignment</a>
   
+    <li><a href="../../../../Bio/DB/Pileup.html">Bio::DB::Pileup</a>
+  
     <li><a href="../../../../Bio/DB/SAM.html">Bio::DB::SAM</a>
   
     <li><a href="../../../../Bio/DB/SAM/Library.html">Bio::DB::SAM::Library</a>
@@ -113,11 +115,9 @@
   
     <li><a href="../../../../Bio/DB/Tag.html">Bio::DB::Tag</a>
   
-    <li><a href="../../../../LibC.html">LibC</a>
-  
-    <li><a href="../../../../Pileup.html">Pileup</a>
+    <li><a href="../../../../Bio/DB/Vcf.html">Bio::DB::Vcf</a>
   
-    <li><a href="../../../../Vcf.html">Vcf</a>
+    <li><a href="../../../../LibC.html">LibC</a>
   
   </ul>
 </nav>

data/doc/Bio/DB/SAM/Tools/SamfileT.html

@@ -89,6 +89,8 @@
   
     <li><a href="../../../../Bio/DB/Alignment.html">Bio::DB::Alignment</a>
   
+    <li><a href="../../../../Bio/DB/Pileup.html">Bio::DB::Pileup</a>
+  
     <li><a href="../../../../Bio/DB/SAM.html">Bio::DB::SAM</a>
   
     <li><a href="../../../../Bio/DB/SAM/Library.html">Bio::DB::SAM::Library</a>
@@ -113,11 +115,9 @@
   
     <li><a href="../../../../Bio/DB/Tag.html">Bio::DB::Tag</a>
   
-    <li><a href="../../../../LibC.html">LibC</a>
-  
-    <li><a href="../../../../Pileup.html">Pileup</a>
+    <li><a href="../../../../Bio/DB/Vcf.html">Bio::DB::Vcf</a>
   
-    <li><a href="../../../../Vcf.html">Vcf</a>
+    <li><a href="../../../../LibC.html">LibC</a>
   
   </ul>
 </nav>

data/doc/Bio/DB/SAM/Tools/SamfileTX.html

@@ -89,6 +89,8 @@
   
     <li><a href="../../../../Bio/DB/Alignment.html">Bio::DB::Alignment</a>
   
+    <li><a href="../../../../Bio/DB/Pileup.html">Bio::DB::Pileup</a>
+  
     <li><a href="../../../../Bio/DB/SAM.html">Bio::DB::SAM</a>
   
     <li><a href="../../../../Bio/DB/SAM/Library.html">Bio::DB::SAM::Library</a>
@@ -113,11 +115,9 @@
   
     <li><a href="../../../../Bio/DB/Tag.html">Bio::DB::Tag</a>
   
-    <li><a href="../../../../LibC.html">LibC</a>
-  
-    <li><a href="../../../../Pileup.html">Pileup</a>
+    <li><a href="../../../../Bio/DB/Vcf.html">Bio::DB::Vcf</a>
   
-    <li><a href="../../../../Vcf.html">Vcf</a>
+    <li><a href="../../../../LibC.html">LibC</a>
   
   </ul>
 </nav>

data/doc/Bio/DB/SAMException.html

@@ -99,6 +99,8 @@
   
     <li><a href="../../Bio/DB/Alignment.html">Bio::DB::Alignment</a>
   
+    <li><a href="../../Bio/DB/Pileup.html">Bio::DB::Pileup</a>
+  
     <li><a href="../../Bio/DB/SAM.html">Bio::DB::SAM</a>
   
     <li><a href="../../Bio/DB/SAM/Library.html">Bio::DB::SAM::Library</a>
@@ -123,11 +125,9 @@
   
     <li><a href="../../Bio/DB/Tag.html">Bio::DB::Tag</a>
   
-    <li><a href="../../LibC.html">LibC</a>
-  
-    <li><a href="../../Pileup.html">Pileup</a>
+    <li><a href="../../Bio/DB/Vcf.html">Bio::DB::Vcf</a>
   
-    <li><a href="../../Vcf.html">Vcf</a>
+    <li><a href="../../LibC.html">LibC</a>
   
   </ul>
 </nav>
@@ -176,7 +176,7 @@
 
           
           <div class="method-source-code" id="new-source">
-            <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 638</span>
+            <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 639</span>
 <span class="ruby-keyword">def</span> <span class="ruby-identifier">initialize</span>()
 
 <span class="ruby-keyword">end</span></pre>

data/doc/Bio/DB/Tag.html

@@ -99,6 +99,8 @@
   
     <li><a href="../../Bio/DB/Alignment.html">Bio::DB::Alignment</a>
   
+    <li><a href="../../Bio/DB/Pileup.html">Bio::DB::Pileup</a>
+  
     <li><a href="../../Bio/DB/SAM.html">Bio::DB::SAM</a>
   
     <li><a href="../../Bio/DB/SAM/Library.html">Bio::DB::SAM::Library</a>
@@ -123,11 +125,9 @@
   
     <li><a href="../../Bio/DB/Tag.html">Bio::DB::Tag</a>
   
-    <li><a href="../../LibC.html">LibC</a>
-  
-    <li><a href="../../Pileup.html">Pileup</a>
+    <li><a href="../../Bio/DB/Vcf.html">Bio::DB::Vcf</a>
   
-    <li><a href="../../Vcf.html">Vcf</a>
+    <li><a href="../../LibC.html">LibC</a>
   
   </ul>
 </nav>
@@ -222,7 +222,7 @@
 
           
           <div class="method-source-code" id="set-source">
-            <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 539</span>
+            <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 540</span>
 <span class="ruby-keyword">def</span> <span class="ruby-identifier">set</span>(<span class="ruby-identifier">str</span>)
   <span class="ruby-identifier">v</span> = <span class="ruby-identifier">str</span>.<span class="ruby-identifier">split</span>(<span class="ruby-string">&quot;:&quot;</span>)
   <span class="ruby-ivar">@tag</span>   = <span class="ruby-identifier">v</span>[<span class="ruby-value">0</span>]

data/doc/Bio/DB/Vcf.html

@@ -0,0 +1,467 @@
+<!DOCTYPE html>
+
+<html>
+<head>
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+<title>Class: Bio::DB::Vcf</title>
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+  <ul>
+    <li>lib/bio/db/vcf.rb
+  </ul>
+</nav>
+
+    
+  </div>
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+    
+    <li><a href="#method-i-int_or_raw">#int_or_raw</a>
+    
+    <li><a href="#method-i-parse_line">#parse_line</a>
+    
+  </ul>
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+  
+    <li><a href="../../Bio/DB/Vcf.html">Bio::DB::Vcf</a>
+  
+    <li><a href="../../LibC.html">LibC</a>
+  
+  </ul>
+</nav>
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+  </div>
+</nav>
+
+<div id="documentation">
+  <h1 class="class">class Bio::DB::Vcf</h1>
+
+  <div id="description" class="description">
+    
+  </div><!-- description -->
+
+  
+  
+  
+  <section id="5Buntitled-5D" class="documentation-section">
+    
+
+    
+
+    
+
+    
+    <!-- Attributes -->
+    <section id="attribute-method-details" class="method-section section">
+      <h3 class="section-header">Attributes</h3>
+
+      
+      <div id="attribute-i-alt" class="method-detail">
+        <div class="method-heading attribute-method-heading">
+          <span class="method-name">alt</span><span
+            class="attribute-access-type">[RW]</span>
+        </div>
+
+        <div class="method-description">
+        
+        
+        
+        </div>
+      </div>
+      
+      <div id="attribute-i-chrom" class="method-detail">
+        <div class="method-heading attribute-method-heading">
+          <span class="method-name">chrom</span><span
+            class="attribute-access-type">[RW]</span>
+        </div>
+
+        <div class="method-description">
+        
+        
+        
+        </div>
+      </div>
+      
+      <div id="attribute-i-filter" class="method-detail">
+        <div class="method-heading attribute-method-heading">
+          <span class="method-name">filter</span><span
+            class="attribute-access-type">[RW]</span>
+        </div>
+
+        <div class="method-description">
+        
+        
+        
+        </div>
+      </div>
+      
+      <div id="attribute-i-format" class="method-detail">
+        <div class="method-heading attribute-method-heading">
+          <span class="method-name">format</span><span
+            class="attribute-access-type">[RW]</span>
+        </div>
+
+        <div class="method-description">
+        
+        
+        
+        </div>
+      </div>
+      
+      <div id="attribute-i-id" class="method-detail">
+        <div class="method-heading attribute-method-heading">
+          <span class="method-name">id</span><span
+            class="attribute-access-type">[RW]</span>
+        </div>
+
+        <div class="method-description">
+        
+        
+        
+        </div>
+      </div>
+      
+      <div id="attribute-i-info" class="method-detail">
+        <div class="method-heading attribute-method-heading">
+          <span class="method-name">info</span><span
+            class="attribute-access-type">[RW]</span>
+        </div>
+
+        <div class="method-description">
+        
+        
+        
+        </div>
+      </div>
+      
+      <div id="attribute-i-pos" class="method-detail">
+        <div class="method-heading attribute-method-heading">
+          <span class="method-name">pos</span><span
+            class="attribute-access-type">[RW]</span>
+        </div>
+
+        <div class="method-description">
+        
+        
+        
+        </div>
+      </div>
+      
+      <div id="attribute-i-qual" class="method-detail">
+        <div class="method-heading attribute-method-heading">
+          <span class="method-name">qual</span><span
+            class="attribute-access-type">[RW]</span>
+        </div>
+
+        <div class="method-description">
+        
+        
+        
+        </div>
+      </div>
+      
+      <div id="attribute-i-ref" class="method-detail">
+        <div class="method-heading attribute-method-heading">
+          <span class="method-name">ref</span><span
+            class="attribute-access-type">[RW]</span>
+        </div>
+
+        <div class="method-description">
+        
+        
+        
+        </div>
+      </div>
+      
+      <div id="attribute-i-samples" class="method-detail">
+        <div class="method-heading attribute-method-heading">
+          <span class="method-name">samples</span><span
+            class="attribute-access-type">[RW]</span>
+        </div>
+
+        <div class="method-description">
+        
+        
+        
+        </div>
+      </div>
+      
+    </section><!-- attribute-method-details -->
+    
+
+    <!-- Methods -->
+    
+     <section id="public-class-5Buntitled-5D-method-details" class="method-section section">
+      <h3 class="section-header">Public Class Methods</h3>
+
+    
+      <div id="method-c-new" class="method-detail ">
+        
+        <div class="method-heading">
+          <span class="method-name">new</span><span
+            class="method-args">(line=nil, sample_names=nil)</span>
+          <span class="method-click-advice">click to toggle source</span>
+        </div>
+        
+
+        <div class="method-description">
+          
+          <p>create the vcf object, use the ordered list of sample names to label
+samples if provided [‘A’, ‘B’, ‘C’], otherwise uses, 1,2,3 etc vcf =
+Bio::DB::Vcf(“19       111   . A       C     9.6 .       .     GT:HQ      
+0|0:10,10     0|0:10,10   0/1:3,3”)</p>
+          
+
+          
+          <div class="method-source-code" id="new-source">
+            <pre><span class="ruby-comment"># File lib/bio/db/vcf.rb, line 15</span>
+<span class="ruby-keyword">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">line</span>=<span class="ruby-keyword">nil</span>, <span class="ruby-identifier">sample_names</span>=<span class="ruby-keyword">nil</span>)
+  <span class="ruby-ivar">@info</span> = {}
+  <span class="ruby-ivar">@samples</span> = {}
+  <span class="ruby-identifier">parse_line</span>(<span class="ruby-identifier">line</span>, <span class="ruby-identifier">sample_names</span>) <span class="ruby-keyword">if</span> <span class="ruby-identifier">line</span> <span class="ruby-operator">!=</span> <span class="ruby-keyword">nil</span>
+<span class="ruby-keyword">end</span></pre>
+          </div><!-- new-source -->
+          
+        </div>
+
+        
+
+        
+      </div><!-- new-method -->
+
+    
+    </section><!-- public-class-method-details -->
+  
+     <section id="public-instance-5Buntitled-5D-method-details" class="method-section section">
+      <h3 class="section-header">Public Instance Methods</h3>
+
+    
+      <div id="method-i-int_or_raw" class="method-detail ">
+        
+        <div class="method-heading">
+          <span class="method-name">int_or_raw</span><span
+            class="method-args">(x)</span>
+          <span class="method-click-advice">click to toggle source</span>
+        </div>
+        
+
+        <div class="method-description">
+          
+          
+          
+
+          
+          <div class="method-source-code" id="int_or_raw-source">
+            <pre><span class="ruby-comment"># File lib/bio/db/vcf.rb, line 21</span>
+<span class="ruby-keyword">def</span> <span class="ruby-identifier">int_or_raw</span>(<span class="ruby-identifier">x</span>)
+  <span class="ruby-constant">Integer</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">x</span>) <span class="ruby-keyword">rescue</span> <span class="ruby-identifier">x</span>
+<span class="ruby-keyword">end</span></pre>
+          </div><!-- int_or_raw-source -->
+          
+        </div>
+
+        
+
+        
+      </div><!-- int_or_raw-method -->
+
+    
+      <div id="method-i-parse_line" class="method-detail ">
+        
+        <div class="method-heading">
+          <span class="method-name">parse_line</span><span
+            class="method-args">(line, sample_names=nil)</span>
+          <span class="method-click-advice">click to toggle source</span>
+        </div>
+        
+
+        <div class="method-description">
+          
+          <p>gets the info in the <a href="Vcf.html">Vcf</a> lines and parses it,
+setting the attributes</p>
+          
+
+          
+          <div class="method-source-code" id="parse_line-source">
+            <pre><span class="ruby-comment"># File lib/bio/db/vcf.rb, line 26</span>
+<span class="ruby-keyword">def</span> <span class="ruby-identifier">parse_line</span>(<span class="ruby-identifier">line</span>, <span class="ruby-identifier">sample_names</span>=<span class="ruby-keyword">nil</span>)
+  <span class="ruby-keyword">return</span> <span class="ruby-keyword">false</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">line</span>[<span class="ruby-value">0</span>,<span class="ruby-value">1</span>] <span class="ruby-operator">==</span> <span class="ruby-string">'#'</span>
+
+  <span class="ruby-identifier">f</span> = <span class="ruby-identifier">line</span>.<span class="ruby-identifier">chomp</span>.<span class="ruby-identifier">split</span>(<span class="ruby-string">&quot;\t&quot;</span>, <span class="ruby-value">-1</span>)
+  <span class="ruby-identifier">raise</span> <span class="ruby-string">&quot;VCF lines must have at least 8 fields&quot;</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">f</span>.<span class="ruby-identifier">size</span> <span class="ruby-operator">&lt;</span> <span class="ruby-value">8</span>
+  <span class="ruby-ivar">@chrom</span> = <span class="ruby-identifier">f</span>[<span class="ruby-value">0</span>]
+  <span class="ruby-ivar">@pos</span> = <span class="ruby-identifier">f</span>[<span class="ruby-value">1</span>].<span class="ruby-identifier">to_i</span>
+  <span class="ruby-ivar">@id</span> =  <span class="ruby-string">'.'</span> <span class="ruby-operator">==</span> <span class="ruby-identifier">f</span>[<span class="ruby-value">2</span>] <span class="ruby-operator">?</span> <span class="ruby-keyword">nil</span> <span class="ruby-operator">:</span> <span class="ruby-identifier">f</span>[<span class="ruby-value">2</span>]
+  <span class="ruby-ivar">@ref</span> = <span class="ruby-identifier">f</span>[<span class="ruby-value">3</span>]
+  <span class="ruby-ivar">@alt</span> = <span class="ruby-identifier">f</span>[<span class="ruby-value">4</span>]
+  <span class="ruby-ivar">@qual</span> = <span class="ruby-identifier">f</span>[<span class="ruby-value">5</span>].<span class="ruby-identifier">to_f</span>
+  <span class="ruby-ivar">@filter</span> = <span class="ruby-string">'.'</span> <span class="ruby-operator">==</span> <span class="ruby-identifier">f</span>[<span class="ruby-value">6</span>] <span class="ruby-operator">?</span> <span class="ruby-keyword">nil</span> <span class="ruby-operator">:</span> <span class="ruby-identifier">f</span>[<span class="ruby-value">6</span>]
+
+  <span class="ruby-ivar">@info</span> = <span class="ruby-string">'.'</span> <span class="ruby-operator">==</span> <span class="ruby-identifier">f</span>[<span class="ruby-value">7</span>] <span class="ruby-operator">?</span> <span class="ruby-keyword">nil</span> <span class="ruby-operator">:</span> {}
+  <span class="ruby-keyword">if</span> <span class="ruby-ivar">@info</span>
+    <span class="ruby-identifier">info_vec</span> = <span class="ruby-identifier">f</span>[<span class="ruby-value">7</span>].<span class="ruby-identifier">split</span>(<span class="ruby-string">&quot;;&quot;</span>)
+    <span class="ruby-identifier">info_vec</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">x</span><span class="ruby-operator">|</span>
+      <span class="ruby-identifier">keyval</span> = <span class="ruby-identifier">x</span>.<span class="ruby-identifier">split</span>(<span class="ruby-string">&quot;=&quot;</span>, <span class="ruby-value">-1</span>)
+      <span class="ruby-keyword">if</span> <span class="ruby-identifier">keyval</span>.<span class="ruby-identifier">size</span> <span class="ruby-operator">==</span> <span class="ruby-value">2</span> <span class="ruby-comment"># If it's key=value</span>
+        <span class="ruby-ivar">@info</span>[<span class="ruby-identifier">keyval</span>[<span class="ruby-value">0</span>]] = <span class="ruby-identifier">keyval</span>[<span class="ruby-value">1</span>]
+      <span class="ruby-keyword">else</span> <span class="ruby-comment"># Otherwise, it's just a flag</span>
+        <span class="ruby-ivar">@info</span>[<span class="ruby-identifier">x</span>] = <span class="ruby-keyword">nil</span>
+      <span class="ruby-keyword">end</span>
+    <span class="ruby-keyword">end</span>
+  <span class="ruby-keyword">end</span>
+
+  <span class="ruby-ivar">@samples</span> = {}
+  <span class="ruby-keyword">return</span> <span class="ruby-keyword">true</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">f</span>.<span class="ruby-identifier">size</span> <span class="ruby-operator">==</span> <span class="ruby-value">8</span>  <span class="ruby-comment"># Has just upto info</span>
+  <span class="ruby-identifier">raise</span> <span class="ruby-string">&quot;Can't have format with no samples&quot;</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">f</span>.<span class="ruby-identifier">size</span> <span class="ruby-operator">==</span> <span class="ruby-value">9</span>
+  
+  <span class="ruby-ivar">@format</span> = <span class="ruby-identifier">f</span>[<span class="ruby-value">8</span>]
+
+  <span class="ruby-identifier">sample_keys</span> = <span class="ruby-ivar">@format</span>.<span class="ruby-identifier">split</span>(<span class="ruby-string">&quot;:&quot;</span>)
+
+  <span class="ruby-identifier">num_samples</span> = <span class="ruby-identifier">f</span>.<span class="ruby-identifier">size</span> <span class="ruby-operator">-</span> <span class="ruby-value">9</span> <span class="ruby-comment"># How many fields are past the format</span>
+
+  <span class="ruby-keyword">if</span> <span class="ruby-identifier">sample_names</span> <span class="ruby-operator">==</span> <span class="ruby-keyword">nil</span> <span class="ruby-comment"># Make the sample names just [&quot;1&quot;, &quot;2&quot;, ... , &quot;num_samples}&quot;</span>
+    <span class="ruby-identifier">sample_names</span> = (<span class="ruby-value">1</span><span class="ruby-operator">..</span><span class="ruby-identifier">num_samples</span>).<span class="ruby-identifier">to_a</span>.<span class="ruby-identifier">map</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">i</span><span class="ruby-operator">|</span> <span class="ruby-identifier">i</span>.<span class="ruby-identifier">to_s</span>} 
+  <span class="ruby-keyword">elsif</span> <span class="ruby-identifier">sample_names</span>.<span class="ruby-identifier">size</span> <span class="ruby-operator">!=</span> <span class="ruby-identifier">num_samples</span>
+    <span class="ruby-identifier">raise</span> <span class="ruby-node">&quot;Unexpected number of samples (#{num_samples}) based on the provided sample names (#{sample_names.inspect})&quot;</span>
+  <span class="ruby-keyword">end</span>
+
+  <span class="ruby-identifier">sample_names</span>.<span class="ruby-identifier">each_with_index</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">sample_name</span>, <span class="ruby-identifier">sample_index</span><span class="ruby-operator">|</span>
+    <span class="ruby-identifier">i</span> = <span class="ruby-identifier">sample_index</span> <span class="ruby-operator">+</span> <span class="ruby-value">9</span> <span class="ruby-comment"># index into columns (f)</span>
+    <span class="ruby-identifier">sample_values</span> = <span class="ruby-identifier">f</span>[<span class="ruby-identifier">i</span>].<span class="ruby-identifier">split</span>(<span class="ruby-string">&quot;:&quot;</span>)
+    <span class="ruby-identifier">raise</span> <span class="ruby-node">&quot;Expected number of sample values to be &lt;= number of sample keys in FORMAT column Format=#{@format} but sample=#{f[i]}&quot;</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">sample_values</span>.<span class="ruby-identifier">size</span> <span class="ruby-operator">&gt;</span> <span class="ruby-identifier">sample_keys</span>.<span class="ruby-identifier">size</span>
+    <span class="ruby-ivar">@samples</span>[<span class="ruby-identifier">sample_name</span>] = {}
+    <span class="ruby-identifier">sample_keys</span>.<span class="ruby-identifier">each_with_index</span> {<span class="ruby-operator">|</span><span class="ruby-identifier">key</span>, <span class="ruby-identifier">value_index</span><span class="ruby-operator">|</span> <span class="ruby-ivar">@samples</span>[<span class="ruby-identifier">sample_name</span>][<span class="ruby-identifier">key</span>] = <span class="ruby-identifier">sample_values</span>[<span class="ruby-identifier">value_index</span>] <span class="ruby-operator">||</span> <span class="ruby-string">&quot;&quot;</span>}
+  <span class="ruby-keyword">end</span>
+  
+  <span class="ruby-keyword">return</span> <span class="ruby-keyword">true</span>;
+<span class="ruby-keyword">end</span></pre>
+          </div><!-- parse_line-source -->
+          
+        </div>
+
+        
+
+        
+      </div><!-- parse_line-method -->
+
+    
+    </section><!-- public-instance-method-details -->
+  
+  </section><!-- 5Buntitled-5D -->
+
+</div><!-- documentation -->
+
+
+<footer id="validator-badges">
+  <p><a href="http://validator.w3.org/check/referer">[Validate]</a>
+  <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 3.11.
+  <p>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish Rdoc Generator</a> 3.
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