bio-samtools 0.2.5 → 0.3.0

data/README.rdoc

@@ -13,27 +13,14 @@ This project was born from the need to add support of BAM files to
 the gee_fu genome browser (http://github.com/danmaclean/gee_fu). 
 
 == Installation
-At the moment, the only way to "install" the module is to copy it to copy the content 
-of the lib folder on any lib folder you have. You must also copy your libbam.a (linux)
-or libbam.dll (windows) from samtools. If you have a Mac, add the following variable
-to the makefile of samtools
-
-DYFLAGS 	= -dynamiclib -lz
-
-and the following target:
-dylib: libbam.dylib
-libbam.dylib:$(LOBJS)
-		$(CC) $(CFLAGS) $(DYFLAGS) -o libbam.dylib $(LOBJS)
-
-Then, run 
-
-make dylib
-
-Finally, you copy the .dylib file to your lib folder. 
+'gem install bio-samtools'
 
 == Usage
-The easiest way to see in "action" samtools-ruby to call
-rake test. 
+The easiest way to see bio-samtools in action is to try the tests
+rake basic_test 
+rake pileup_test
+
+See doc/tutorial.html or doc/tutorial.pdf for a walkthrough tutorial
 
 
 == Dependencies:
@@ -50,9 +37,9 @@ There are two known segmentation faults at the moment
 If this is not the problem, or you have any other question,  don´t hesitate on 
 dropping a line to
 Ricardo dot Ramirez-Gonzalez at bbsrc dot ac dot uk
+dan.maclean@tsl.ac.uk
 
 == TODO
--Write a gem to install it
 -Filter to the fetching algorithm (give a condition that has to be satisfied to add the alignment to the list)
 -Examples of how to use it, besides the test folder
 -Operating system independent, DONE ( test needed)

data/Rakefile

@@ -32,6 +32,17 @@ Jeweler::Tasks.new do |gem|
 end
 Jeweler::RubygemsDotOrgTasks.new
 
+desc "Basic Functionality Test"
+task :basic_test do
+  ruby "test/basictest.rb"
+end
+
+
+desc "Test the Pileup class"
+task :pileup_test do 
+  ruby "test/pileup.rb"
+end
+
 require 'rake/testtask'
 Rake::TestTask.new(:test) do |test|
   test.libs << 'lib' << 'test'

data/VERSION

@@ -1 +1 @@
-0.2.5
+0.3.0

data/bio-samtools.gemspec

@@ -5,7 +5,7 @@
 
 Gem::Specification.new do |s|
   s.name = %q{bio-samtools}
-  s.version = "0.2.5"
+  s.version = "0.3.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = [%q{Ricardo Ramirez-Gonzalez}, %q{Dan MacLean}, %q{Raoul J.P. Bonnal}]
@@ -29,6 +29,70 @@ Gem::Specification.new do |s|
     "Rakefile",
     "VERSION",
     "bio-samtools.gemspec",
+    "doc/basic_styles.css",
+    "doc/classes/Bio.html",
+    "doc/classes/Bio/DB.html",
+    "doc/classes/Bio/DB/Alignment.html",
+    "doc/classes/Bio/DB/Alignment.src/M000012.html",
+    "doc/classes/Bio/DB/Alignment.src/M000013.html",
+    "doc/classes/Bio/DB/Alignment.src/M000014.html",
+    "doc/classes/Bio/DB/Alignment.src/M000015.html",
+    "doc/classes/Bio/DB/SAM.html",
+    "doc/classes/Bio/DB/SAM/Library.html",
+    "doc/classes/Bio/DB/SAM/Library.src/M000006.html",
+    "doc/classes/Bio/DB/SAM/Tools.html",
+    "doc/classes/Bio/DB/SAM/Tools.src/M000007.html",
+    "doc/classes/Bio/DB/SAM/Tools/Bam1CoreT.html",
+    "doc/classes/Bio/DB/SAM/Tools/Bam1T.html",
+    "doc/classes/Bio/DB/SAM/Tools/Bam1T.src/M000010.html",
+    "doc/classes/Bio/DB/SAM/Tools/BamHeaderT.html",
+    "doc/classes/Bio/DB/SAM/Tools/BamHeaderT.src/M000008.html",
+    "doc/classes/Bio/DB/SAM/Tools/BamHeaderT.src/M000009.html",
+    "doc/classes/Bio/DB/SAM/Tools/BamPileup1T.html",
+    "doc/classes/Bio/DB/SAM/Tools/SamfileT.html",
+    "doc/classes/Bio/DB/SAM/Tools/SamfileTX.html",
+    "doc/classes/Bio/DB/SAMException.html",
+    "doc/classes/Bio/DB/SAMException.src/M000016.html",
+    "doc/classes/Bio/DB/Sam.src/M000017.html",
+    "doc/classes/Bio/DB/Sam.src/M000018.html",
+    "doc/classes/Bio/DB/Sam.src/M000019.html",
+    "doc/classes/Bio/DB/Sam.src/M000020.html",
+    "doc/classes/Bio/DB/Sam.src/M000021.html",
+    "doc/classes/Bio/DB/Sam.src/M000022.html",
+    "doc/classes/Bio/DB/Sam.src/M000023.html",
+    "doc/classes/Bio/DB/Sam.src/M000024.html",
+    "doc/classes/Bio/DB/Sam.src/M000025.html",
+    "doc/classes/Bio/DB/Sam.src/M000026.html",
+    "doc/classes/Bio/DB/Sam.src/M000027.html",
+    "doc/classes/Bio/DB/Sam.src/M000028.html",
+    "doc/classes/Bio/DB/Sam.src/M000029.html",
+    "doc/classes/Bio/DB/Sam.src/M000030.html",
+    "doc/classes/Bio/DB/Sam.src/M000031.html",
+    "doc/classes/Bio/DB/Sam.src/M000032.html",
+    "doc/classes/Bio/DB/Tag.html",
+    "doc/classes/Bio/DB/Tag.src/M000011.html",
+    "doc/classes/LibC.html",
+    "doc/classes/Pileup.html",
+    "doc/classes/Pileup.src/M000001.html",
+    "doc/classes/Pileup.src/M000002.html",
+    "doc/classes/Pileup.src/M000003.html",
+    "doc/classes/Pileup.src/M000004.html",
+    "doc/classes/Pileup.src/M000005.html",
+    "doc/created.rid",
+    "doc/files/lib/bio-samtools_rb.html",
+    "doc/files/lib/bio/db/sam/bam_rb.html",
+    "doc/files/lib/bio/db/sam/faidx_rb.html",
+    "doc/files/lib/bio/db/sam/library_rb.html",
+    "doc/files/lib/bio/db/sam/pileup_rb.html",
+    "doc/files/lib/bio/db/sam/sam_rb.html",
+    "doc/files/lib/bio/db/sam_rb.html",
+    "doc/fr_class_index.html",
+    "doc/fr_file_index.html",
+    "doc/fr_method_index.html",
+    "doc/index.html",
+    "doc/rdoc-style.css",
+    "doc/tutorial.html",
+    "doc/tutorial.pdf",
     "ext/mkrf_conf.rb",
     "lib/bio-samtools.rb",
     "lib/bio/.DS_Store",
@@ -38,12 +102,14 @@ Gem::Specification.new do |s|
     "lib/bio/db/sam/external/VERSION",
     "lib/bio/db/sam/faidx.rb",
     "lib/bio/db/sam/library.rb",
+    "lib/bio/db/sam/pileup.rb",
     "lib/bio/db/sam/sam.rb",
     "test/basictest.rb",
     "test/coverage.rb",
     "test/coverage_plot.rb",
     "test/feature.rb",
     "test/helper.rb",
+    "test/pileup.rb",
     "test/samples/small/ids2.txt",
     "test/samples/small/sorted.bam",
     "test/samples/small/test",

data/doc/basic_styles.css

@@ -0,0 +1,31 @@
+/*
+untitled
+
+Created by macleand on 2011-10-14.
+Copyright (c) 2011 Dan MacLean. All rights reserved.
+*/
+#main { margin: 40px 0 60px 0; overflow: hidden; }
+#wrap { width: 800px; margin: 0 auto 50px; }
+body { font: 12px/20px "Helvetica Neue", Helvetica, Arial, sans-serif; color: #555; font-weight: normal; }
+h1 { font-size: 38px; margin: 0 0 10px 0; }
+h2 { font-size: 30px; margin: 0 0 10px 0; }
+h3 { font-size: 24px; margin: 0 0 10px 0; }
+h4 { font-size: 18px; margin: 0 0 10px 0; }
+h5 { font-size: 16px; margin: 0 0 5px 0; }
+h6 { font-size: 14px; margin: 0 0 5px 0; }
+p { margin: 0 0 15px 0; }
+a { text-decoration: none; color: #FF7200; }
+a:hover { color: #222; }
+em { font-style: italic; }
+ul { margin: 0 0 15px 15px; list-style-type: circle; }
+ol { margin: 15px 0 15px 20px; list-style-type: decimal; }
+strong, b { font-weight: bold; }
+.hide { display: none; }
+#header { padding: 55px 0 0 0; margin: 0 0 40px 0; }
+table {border: 1px solid black; text-align:left; padding:5px;}
+th
+{
+background-color:#FF7200;
+padding:5px;
+}
+td {padding: 5px;}

data/doc/classes/Bio.html

@@ -0,0 +1,139 @@
+<?xml version="1.0" encoding="iso-8859-1"?>
+<!DOCTYPE html 
+     PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+     "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+  <title>Module: Bio</title>
+  <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
+  <meta http-equiv="Content-Script-Type" content="text/javascript" />
+  <link rel="stylesheet" href=".././rdoc-style.css" type="text/css" media="screen" />
+  <script type="text/javascript">
+  // <![CDATA[
+
+  function popupCode( url ) {
+    window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
+  }
+
+  function toggleCode( id ) {
+    if ( document.getElementById )
+      elem = document.getElementById( id );
+    else if ( document.all )
+      elem = eval( "document.all." + id );
+    else
+      return false;
+
+    elemStyle = elem.style;
+    
+    if ( elemStyle.display != "block" ) {
+      elemStyle.display = "block"
+    } else {
+      elemStyle.display = "none"
+    }
+
+    return true;
+  }
+  
+  // Make codeblocks hidden by default
+  document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
+  
+  // ]]>
+  </script>
+
+</head>
+<body>
+
+
+
+    <div id="classHeader">
+        <table class="header-table">
+        <tr class="top-aligned-row">
+          <td><strong>Module</strong></td>
+          <td class="class-name-in-header">Bio</td>
+        </tr>
+        <tr class="top-aligned-row">
+            <td><strong>In:</strong></td>
+            <td>
+                <a href="../files/lib/bio/db/sam/bam_rb.html">
+                lib/bio/db/sam/bam.rb
+                </a>
+        <br />
+                <a href="../files/lib/bio/db/sam/faidx_rb.html">
+                lib/bio/db/sam/faidx.rb
+                </a>
+        <br />
+                <a href="../files/lib/bio/db/sam/library_rb.html">
+                lib/bio/db/sam/library.rb
+                </a>
+        <br />
+                <a href="../files/lib/bio/db/sam/sam_rb.html">
+                lib/bio/db/sam/sam.rb
+                </a>
+        <br />
+                <a href="../files/lib/bio/db/sam_rb.html">
+                lib/bio/db/sam.rb
+                </a>
+        <br />
+            </td>
+        </tr>
+
+        </table>
+    </div>
+  <!-- banner header -->
+
+  <div id="bodyContent">
+
+
+
+  <div id="contextContent">
+
+    <div id="description">
+      <pre>
+ sam.rb
+
+ Created by Ricardo Ramirez on 3/25/10.
+</pre>
+<p>
+require &#8216;rubygems&#8217; require&#8216;ffi&#8217; require
+&#8216;bio/db/sam/bam&#8216;
+</p>
+
+    </div>
+
+
+   </div>
+
+
+  </div>
+
+
+    <!-- if includes -->
+
+    <div id="section">
+
+    <div id="class-list">
+      <h3 class="section-bar">Classes and Modules</h3>
+
+      Class <a href="Bio/DB.html" class="link">Bio::DB</a><br />
+
+    </div>
+
+
+
+
+      
+
+
+    <!-- if method_list -->
+
+
+  </div>
+
+
+<div id="validator-badges">
+  <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
+</div>
+
+</body>
+</html>

data/doc/classes/Bio/DB.html

@@ -0,0 +1,137 @@
+<?xml version="1.0" encoding="iso-8859-1"?>
+<!DOCTYPE html 
+     PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+     "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+  <title>Class: Bio::DB</title>
+  <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
+  <meta http-equiv="Content-Script-Type" content="text/javascript" />
+  <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
+  <script type="text/javascript">
+  // <![CDATA[
+
+  function popupCode( url ) {
+    window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
+  }
+
+  function toggleCode( id ) {
+    if ( document.getElementById )
+      elem = document.getElementById( id );
+    else if ( document.all )
+      elem = eval( "document.all." + id );
+    else
+      return false;
+
+    elemStyle = elem.style;
+    
+    if ( elemStyle.display != "block" ) {
+      elemStyle.display = "block"
+    } else {
+      elemStyle.display = "none"
+    }
+
+    return true;
+  }
+  
+  // Make codeblocks hidden by default
+  document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
+  
+  // ]]>
+  </script>
+
+</head>
+<body>
+
+
+
+    <div id="classHeader">
+        <table class="header-table">
+        <tr class="top-aligned-row">
+          <td><strong>Class</strong></td>
+          <td class="class-name-in-header">Bio::DB</td>
+        </tr>
+        <tr class="top-aligned-row">
+            <td><strong>In:</strong></td>
+            <td>
+                <a href="../../files/lib/bio/db/sam/bam_rb.html">
+                lib/bio/db/sam/bam.rb
+                </a>
+        <br />
+                <a href="../../files/lib/bio/db/sam/faidx_rb.html">
+                lib/bio/db/sam/faidx.rb
+                </a>
+        <br />
+                <a href="../../files/lib/bio/db/sam/library_rb.html">
+                lib/bio/db/sam/library.rb
+                </a>
+        <br />
+                <a href="../../files/lib/bio/db/sam/sam_rb.html">
+                lib/bio/db/sam/sam.rb
+                </a>
+        <br />
+                <a href="../../files/lib/bio/db/sam_rb.html">
+                lib/bio/db/sam.rb
+                </a>
+        <br />
+            </td>
+        </tr>
+
+        <tr class="top-aligned-row">
+            <td><strong>Parent:</strong></td>
+            <td>
+                Object
+            </td>
+        </tr>
+        </table>
+    </div>
+  <!-- banner header -->
+
+  <div id="bodyContent">
+
+
+
+  <div id="contextContent">
+
+
+
+   </div>
+
+
+  </div>
+
+
+    <!-- if includes -->
+
+    <div id="section">
+
+    <div id="class-list">
+      <h3 class="section-bar">Classes and Modules</h3>
+
+      Module <a href="DB/SAM.html" class="link">Bio::DB::SAM</a><br />
+Class <a href="DB/Alignment.html" class="link">Bio::DB::Alignment</a><br />
+Class <a href="DB/SAMException.html" class="link">Bio::DB::SAMException</a><br />
+Class <a href="DB/Sam.html" class="link">Bio::DB::Sam</a><br />
+Class <a href="DB/Tag.html" class="link">Bio::DB::Tag</a><br />
+
+    </div>
+
+
+
+
+      
+
+
+    <!-- if method_list -->
+
+
+  </div>
+
+
+<div id="validator-badges">
+  <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
+</div>
+
+</body>
+</html>