bio-samtools 0.4.2 → 0.5.0

data/doc/LICENSE_txt.html

@@ -65,6 +65,8 @@
   
     <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>
@@ -89,11 +91,9 @@
   
     <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>
@@ -106,18 +106,17 @@
 <p>Copyright © 2011 Raoul J.P. Bonnal</p>
 
 <p>Permission is hereby granted, free of charge, to any person obtaining a
-copy of this software and associated documentation files (the
-“Software”), to deal in the Software without restriction, including
-without limitation the rights to use, copy, modify, merge, publish,
-distribute, sublicense, and/or sell copies of the Software, and to permit
-persons to whom the Software is furnished to do so, subject to the
-following conditions:</p>
+copy of this software and associated documentation files (the “Software”),
+to deal in the Software without restriction, including without limitation
+the rights to use, copy, modify, merge, publish, distribute, sublicense,
+and/or sell copies of the Software, and to permit persons to whom the
+Software is furnished to do so, subject to the following conditions:</p>
 
 <p>The above copyright notice and this permission notice shall be included in
 all copies or substantial portions of the Software.</p>
 
-<p>THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS
-OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+<p>THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
@@ -143,11 +142,10 @@ of this license document, but changing it is not allowed.
 
 <p>to take away your freedom to share and change the works.  By contrast, the
 GNU General Public License is intended to guarantee your freedom to share
-and change all versions of a program–to make sure it remains free
-software for all its users.  We, the Free Software Foundation, use the GNU
-General Public License for most of our software; it applies also to any
-other work released this way by its authors.  You can apply it to your
-programs, too.</p>
+and change all versions of a program–to make sure it remains free software
+for all its users.  We, the Free Software Foundation, use the GNU General
+Public License for most of our software; it applies also to any other work
+released this way by its authors.  You can apply it to your programs, too.</p>
 
 <pre>When we speak of free software, we are referring to freedom, not</pre>
 
@@ -258,8 +256,8 @@ list meets this criterion.</p>
 
 The &quot;source code&quot; for a work means the preferred form of the work</pre>
 
-<p>for making modifications to it.  “Object code” means any non-source
-form of a work.</p>
+<p>for making modifications to it.  “Object code” means any non-source form of
+a work.</p>
 
 <pre>A &quot;Standard Interface&quot; means an interface that either is an official</pre>
 
@@ -273,11 +271,11 @@ widely used among developers working in that language.</p>
 packaging a Major Component, but which is not part of that Major Component,
 and (b) serves only to enable use of the work with that Major Component, or
 to implement a Standard Interface for which an implementation is available
-to the public in source code form.  A “Major Component”, in this
-context, means a major essential component (kernel, window system, and so
-on) of the specific operating system (if any) on which the executable work
-runs, or a compiler used to produce the work, or an object code interpreter
-used to run it.</p>
+to the public in source code form.  A “Major Component”, in this context,
+means a major essential component (kernel, window system, and so on) of the
+specific operating system (if any) on which the executable work runs, or a
+compiler used to produce the work, or an object code interpreter used to
+run it.</p>
 
 <pre>The &quot;Corresponding Source&quot; for a work in object code form means all</pre>
 
@@ -341,8 +339,8 @@ prohibiting or restricting circumvention of such measures.</p>
 <p>circumvention of technological measures to the extent such circumvention is
 effected by exercising rights under this License with respect to the
 covered work, and you disclaim any intention to limit operation or
-modification of the work as a means of enforcing, against the work’s
-users, your or third parties’ legal rights to forbid circumvention of
+modification of the work as a means of enforcing, against the work’s users,
+your or third parties’ legal rights to forbid circumvention of
 technological measures.</p>
 
 <pre>4. Conveying Verbatim Copies.
@@ -392,11 +390,11 @@ A compilation of a covered work with other separate and independent</pre>
 
 <p>works, which are not by their nature extensions of the covered work, and
 which are not combined with it such as to form a larger program, in or on a
-volume of a storage or distribution medium, is called an “aggregate” if
-the compilation and its resulting copyright are not used to limit the
-access or legal rights of the compilation’s users beyond what the
-individual works permit.  Inclusion of a covered work in an aggregate does
-not cause this License to apply to the other parts of the aggregate.</p>
+volume of a storage or distribution medium, is called an “aggregate” if the
+compilation and its resulting copyright are not used to limit the access or
+legal rights of the compilation’s users beyond what the individual works
+permit.  Inclusion of a covered work in an aggregate does not cause this
+License to apply to the other parts of the aggregate.</p>
 
 <pre>6. Conveying Non-Source Forms.
 
@@ -458,13 +456,13 @@ conveying the object code work.</p>
 household purposes, or (2) anything designed or sold for incorporation into
 a dwelling.  In determining whether a product is a consumer product,
 doubtful cases shall be resolved in favor of coverage.  For a particular
-product received by a particular user, “normally used” refers to a
-typical or common use of that class of product, regardless of the status of
-the particular user or of the way in which the particular user actually
-uses, or expects or is expected to use, the product.  A product is a
-consumer product regardless of whether the product has substantial
-commercial, industrial or non-consumer uses, unless such uses represent the
-only significant mode of use of the product.</p>
+product received by a particular user, “normally used” refers to a typical
+or common use of that class of product, regardless of the status of the
+particular user or of the way in which the particular user actually uses,
+or expects or is expected to use, the product.  A product is a consumer
+product regardless of whether the product has substantial commercial,
+industrial or non-consumer uses, unless such uses represent the only
+significant mode of use of the product.</p>
 
 <pre>&quot;Installation Information&quot; for a User Product means any methods,</pre>
 
@@ -671,9 +669,9 @@ the contents of its contributor version.</p>
 
 <p>agreement or commitment, however denominated, not to enforce a patent (such
 as an express permission to practice a patent or covenant not to sue for
-patent infringement).  To “grant” such a patent license to a party
-means to make such an agreement or commitment not to enforce a patent
-against the party.</p>
+patent infringement).  To “grant” such a patent license to a party means to
+make such an agreement or commitment not to enforce a patent against the
+party.</p>
 
 <pre>If you convey a covered work, knowingly relying on a patent license,</pre>
 
@@ -684,10 +682,10 @@ you must either (1) cause the Corresponding Source to be so available, or
 (2) arrange to deprive yourself of the benefit of the patent license for
 this particular work, or (3) arrange, in a manner consistent with the
 requirements of this License, to extend the patent license to downstream
-recipients.  “Knowingly relying” means you have actual knowledge that,
-but for the patent license, your conveying the covered work in a country,
-or your recipient’s use of the covered work in a country, would infringe
-one or more identifiable patents in that country that you have reason to
+recipients.  “Knowingly relying” means you have actual knowledge that, but
+for the patent license, your conveying the covered work in a country, or
+your recipient’s use of the covered work in a country, would infringe one
+or more identifiable patents in that country that you have reason to
 believe are valid.</p>
 
 <pre>If, pursuant to or in connection with a single transaction or</pre>
@@ -764,9 +762,9 @@ Foundation.</p>
 
 <pre>If the Program specifies that a proxy can decide which future</pre>
 
-<p>versions of the GNU General Public License can be used, that proxy’s
-public statement of acceptance of a version permanently authorizes you to
-choose that version for the Program.</p>
+<p>versions of the GNU General Public License can be used, that proxy’s public
+statement of acceptance of a version permanently authorizes you to choose
+that version for the Program.</p>
 
 <pre>Later license versions may give you additional or different</pre>
 
@@ -778,12 +776,12 @@ or copyright holder as a result of your choosing to follow a later version.</p>
 THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY</pre>
 
 <p>APPLICABLE LAW.  EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
-HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM “AS IS” WITHOUT
-WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT
-LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
-PARTICULAR PURPOSE.  THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF
-THE PROGRAM IS WITH YOU.  SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME
-THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.</p>
+HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM “AS IS” WITHOUT WARRANTY
+OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE.  THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
+IS WITH YOU.  SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.</p>
 
 <pre>16. Limitation of Liability.
 
@@ -850,15 +848,14 @@ This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
 This is free software, and you are welcome to redistribute it
 under certain conditions; type `show c' for details.</pre>
 
-<p>The hypothetical commands `show w’ and `show c’ should show the
-appropriate parts of the General Public License.  Of course, your
-program’s commands might be different; for a GUI interface, you would use
-an “about box”.</p>
+<p>The hypothetical commands `show w’ and `show c’ should show the appropriate
+parts of the General Public License.  Of course, your program’s commands
+might be different; for a GUI interface, you would use an “about box”.</p>
 
 <pre>You should also get your employer (if you work as a programmer) or school,</pre>
 
-<p>if any, to sign a “copyright disclaimer” for the program, if necessary.
-For more information on this, and how to apply and follow the GNU GPL, see
+<p>if any, to sign a “copyright disclaimer” for the program, if necessary. For
+more information on this, and how to apply and follow the GNU GPL, see
 &lt;<a href="http://www.gnu.org/licenses/">www.gnu.org/licenses/</a>&gt;.</p>
 
 <pre>The GNU General Public License does not permit incorporating your program</pre>

data/doc/LibC.html

@@ -83,6 +83,8 @@
   
     <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>
@@ -107,11 +109,9 @@
   
     <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>
@@ -124,6 +124,8 @@
 
   <div id="description" class="description">
     
+<p>require ‘bio/db/pileup’ require ‘bio/db/vcf’</p>
+
   </div><!-- description -->
 
   

data/doc/created.rid

@@ -1,10 +1,10 @@
-Wed, 09 Nov 2011 21:18:55 +0000
+Fri, 13 Jan 2012 10:07:15 +0000
+./lib/bio/db/pileup.rb	Thu, 12 Jan 2012 15:37:18 +0000
+./lib/bio/db/sam/bam.rb	Thu, 12 Jan 2012 15:31:33 +0000
 ./lib/bio/db/sam/faidx.rb	Wed, 02 Nov 2011 11:50:27 +0000
-./LICENSE.txt	Wed, 02 Nov 2011 11:50:27 +0000
-./lib/bio/db/sam/pileup.rb	Wed, 02 Nov 2011 11:50:27 +0000
-./lib/bio/db/sam/sam.rb	Mon, 07 Nov 2011 10:04:59 +0000
 ./lib/bio/db/sam/library.rb	Wed, 02 Nov 2011 13:28:41 +0000
+./lib/bio/db/sam/sam.rb	Mon, 07 Nov 2011 10:04:59 +0000
+./lib/bio/db/sam.rb	Thu, 12 Jan 2012 15:38:07 +0000
+./lib/bio/db/vcf.rb	Thu, 12 Jan 2012 15:52:37 +0000
 ./lib/bio-samtools.rb	Wed, 02 Nov 2011 16:15:52 +0000
-./lib/bio/db/sam/vcf.rb	Wed, 09 Nov 2011 20:53:50 +0000
-./lib/bio/db/sam/bam.rb	Wed, 02 Nov 2011 13:43:07 +0000
-./lib/bio/db/sam.rb	Wed, 09 Nov 2011 21:03:13 +0000
+./LICENSE.txt	Wed, 02 Nov 2011 11:50:27 +0000

data/doc/index.html

@@ -65,6 +65,8 @@
   
     <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>
@@ -89,11 +91,9 @@
   
     <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/js/search_index.js

@@ -1 +1 @@
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+var search_data = {"index":{"searchIndex":["bio","db","alignment","pileup","sam","library","tools","bam1coret","bam1t","bamheadert","bampileup1t","samfilet","samfiletx","samexception","sam","tag","vcf","libc","average_coverage()","bam_sort()","chromosome_coverage()","close()","deprecated_pileup()","fetch()","fetch_reference()","fetch_with_function()","filename()","finalize()","finalize()","index_stats()","int_or_raw()","load_index()","load_reference()","merge()","mpileup()","mpileup_plus()","new()","new()","new()","new()","new()","non_ref_count()","non_refs()","open()","parse_line()","qname()","query_string()","ref_count()","sam=()","set()","set()","text()","text=()","to_s()","license"],"longSearchIndex":["bio","bio::db","bio::db::alignment","bio::db::pileup","bio::db::sam","bio::db::sam::library","bio::db::sam::tools","bio::db::sam::tools::bam1coret","bio::db::sam::tools::bam1t","bio::db::sam::tools::bamheadert","bio::db::sam::tools::bampileup1t","bio::db::sam::tools::samfilet","bio::db::sam::tools::samfiletx","bio::db::samexception","bio::db::sam","bio::db::tag","bio::db::vcf","libc","bio::db::sam#average_coverage()","bio::db::sam::tools::bam_sort()","bio::db::sam#chromosome_coverage()","bio::db::sam#close()","bio::db::sam#deprecated_pileup()","bio::db::sam#fetch()","bio::db::sam#fetch_reference()","bio::db::sam#fetch_with_function()","bio::db::sam::library::filename()","bio::db::alignment::finalize()","bio::db::sam::finalize()","bio::db::sam#index_stats()","bio::db::vcf#int_or_raw()","bio::db::sam#load_index()","bio::db::sam#load_reference()","bio::db::sam::merge()","bio::db::sam#mpileup()","bio::db::sam#mpileup_plus()","bio::db::alignment::new()","bio::db::pileup::new()","bio::db::samexception::new()","bio::db::sam::new()","bio::db::vcf::new()","bio::db::pileup#non_ref_count()","bio::db::pileup#non_refs()","bio::db::sam#open()","bio::db::vcf#parse_line()","bio::db::sam::tools::bam1t#qname()","bio::db::sam#query_string()","bio::db::pileup#ref_count()","bio::db::alignment#sam=()","bio::db::alignment#set()","bio::db::tag#set()","bio::db::sam::tools::bamheadert#text()","bio::db::sam::tools::bamheadert#text=()","bio::db::sam#to_s()",""],"info":[["Bio","","Bio.html","","<p>Bio::DB::Pileup \n<p>A class representing information in SAMTools pileup format\n<p>Author &mdash; 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data/doc/lib/bio-samtools_rb.html

@@ -65,6 +65,8 @@
   
     <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>
@@ -89,11 +91,9 @@
   
     <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/lib/bio/db/pileup_rb.html

@@ -0,0 +1,171 @@
+<!DOCTYPE html>
+
+<html>
+<head>
+<meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
+
+<title>LICENSE</title>
+
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+    <li><a href="../../../Bio.html">Bio</a>
+  
+    <li><a href="../../../Bio/DB.html">Bio::DB</a>
+  
+    <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>
+  
+    <li><a href="../../../Bio/DB/SAM/Tools.html">Bio::DB::SAM::Tools</a>
+  
+    <li><a href="../../../Bio/DB/SAM/Tools/Bam1CoreT.html">Bio::DB::SAM::Tools::Bam1CoreT</a>
+  
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+  
+    <li><a href="../../../Bio/DB/SAM/Tools/BamHeaderT.html">Bio::DB::SAM::Tools::BamHeaderT</a>
+  
+    <li><a href="../../../Bio/DB/SAM/Tools/BamPileup1T.html">Bio::DB::SAM::Tools::BamPileup1T</a>
+  
+    <li><a href="../../../Bio/DB/SAM/Tools/SamfileT.html">Bio::DB::SAM::Tools::SamfileT</a>
+  
+    <li><a href="../../../Bio/DB/SAM/Tools/SamfileTX.html">Bio::DB::SAM::Tools::SamfileTX</a>
+  
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+  
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+  
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+  
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+</nav>
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+
+<div id="documentation" class="description">
+  
+<h1 id="label-Bio%3A%3ADB%3A%3APileup+"><a href="../../../Bio/DB/Pileup.html">Bio::DB::Pileup</a> </h1>
+
+<p>A class representing information in SAMTools pileup format</p>
+<dl class="rdoc-list note-list"><dt>Author
+<dd>
+<p>Dan MacLean (tsl at dan.maclean.ac.uk)</p>
+</dd></dl>
+
+<p>Pileup is described at <a
+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>.
+Briefly (when you invoke pileup with the -c option):</p>
+<ul><li>
+<p>1 reference sequence name</p>
+</li><li>
+<p>2 reference coordinate</p>
+</li><li>
+<p>(3) reference base, or `*‘ for an indel line</p>
+</li><li>
+<p>(4) genotype where heterozygotes are encoded in the IUB code: M=A/C, R=A/G,
+W=A/T, S=C/G, Y=C/T and K=G/T; indels are indicated by, for example,   +A,
+-A   or +CC/-C. There is no difference between */+A or +A/*.</p>
+</li><li>
+<p>(5) Phred-scaled likelihood that the genotype is wrong, which is also
+called `consensus quality’.</p>
+</li><li>
+<p>(6) Phred-scaled likelihood that the genotype is identical to the
+reference, which is also called `SNP quality’. Suppose the reference base
+is A and in alignment we see 17 G and 3 A. We will get a low consensus
+quality because it is difficult to distinguish an A/G heterozygote from a
+G/G homozygote. We will get a high SNP quality, though, because the
+evidence of a SNP is very strong.</p>
+</li><li>
+<p>(7) root mean square (RMS) mapping quality</p>
+</li><li>
+<p>8 # reads covering the position</p>
+</li><li>
+<p>9 read bases at a SNP line (check the manual page for more information);
+the 1st indel allele otherwise</p>
+</li><li>
+<p>10 base quality at a SNP line; the 2nd indel allele otherwise</p>
+</li><li>
+<p>(11) indel line only: # reads directly supporting the 1st indel allele</p>
+</li><li>
+<p>(12) indel line only: # reads directly supporting the 2nd indel allele</p>
+</li><li>
+<p>(13) indel line only: # reads supporting a third indel allele</p>
+</li></ul>
+
+<p>If pileup is invoked without `-c’, indel lines and columns between 3 and 7
+inclusive will not be outputted.</p>
+
+<p>NB mpileup uses the 6 column output format eg
+“seq2t151tGtGt36t0t99t12t.….……At:9&lt;;;7=&lt;&lt;&lt;&lt;&lt;” Pileup
+provides accessors for all columns (6 or 10 column format) and a few other
+useful methods</p>
+
+</div>
+
+
+
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