bio-samtools 0.4.1 → 0.4.2

data/doc/js/search.js

@@ -0,0 +1,94 @@
+Search = function(data, input, result) {
+  this.data = data;
+  this.$input = $(input);
+  this.$result = $(result);
+
+  this.$current = null;
+  this.$view = this.$result.parent();
+  this.searcher = new Searcher(data.index);
+  this.init();
+}
+
+Search.prototype = $.extend({}, Navigation, new function() {
+  var suid = 1;
+
+  this.init = function() {
+    var _this = this;
+    var observer = function() {
+      _this.search(_this.$input[0].value);
+    };
+    this.$input.keyup(observer);
+    this.$input.click(observer); // mac's clear field
+
+    this.searcher.ready(function(results, isLast) {
+      _this.addResults(results, isLast);
+    })
+
+    this.initNavigation();
+    this.setNavigationActive(false);
+  }
+
+  this.search = function(value, selectFirstMatch) {
+    value = jQuery.trim(value).toLowerCase();
+    if (value) {
+      this.setNavigationActive(true);
+    } else {
+      this.setNavigationActive(false);
+    }
+
+    if (value == '') {
+      this.lastQuery = value;
+      this.$result.empty();
+      this.setNavigationActive(false);
+    } else if (value != this.lastQuery) {
+      this.lastQuery = value;
+      this.firstRun = true;
+      this.searcher.find(value);
+    }
+  }
+
+  this.addResults = function(results, isLast) {
+    var target = this.$result.get(0);
+    if (this.firstRun && (results.length > 0 || isLast)) {
+      this.$current = null;
+      this.$result.empty();
+    }
+
+    for (var i=0, l = results.length; i < l; i++) {
+      target.appendChild(this.renderItem.call(this, results[i]));
+    };
+
+    if (this.firstRun && results.length > 0) {
+      this.firstRun = false;
+      this.$current = $(target.firstChild);
+      this.$current.addClass('current');
+    }
+    if (jQuery.browser.msie) this.$element[0].className += '';
+  }
+
+  this.move = function(isDown) {
+    if (!this.$current) return;
+    var $next = this.$current[isDown ? 'next' : 'prev']();
+    if ($next.length) {
+      this.$current.removeClass('current');
+      $next.addClass('current');
+      this.scrollIntoView($next[0], this.$view[0]);
+      this.$current = $next;
+    }
+    return true;
+  }
+
+  this.hlt = function(html) {
+    return this.escapeHTML(html).
+      replace(/\u0001/g, '<em>').
+      replace(/\u0002/g, '</em>');
+  }
+
+  this.escapeHTML = function(html) {
+    return html.replace(/[&<>]/g, function(c) {
+      return '&#' + c.charCodeAt(0) + ';';
+    });
+  }
+
+});
+

data/doc/js/search_index.js

@@ -0,0 +1 @@
+var search_data = {"index":{"info":[["Bio","","Bio.html","","<p>require ‘rubygems’ require ‘ffi’\n\n<pre class=\"ruby\"><span class=\"ruby-identifier\">require</span> <span class=\"ruby-string\">'bio/db/sam/faidx'</span>\n<span class=\"ruby-identifier\">require</span> <span class=\"ruby-string\">'bio/db/sam/sam'</span>\n</pre>\n<p>require ‘rubygems’ …\n"],["Bio::DB","","Bio/DB.html","",""],["Bio::DB::Alignment","","Bio/DB/Alignment.html","",""],["Bio::DB::SAM","","Bio/DB/SAM.html","",""],["Bio::DB::SAM::Library","","Bio/DB/SAM/Library.html","",""],["Bio::DB::SAM::Tools","","Bio/DB/SAM/Tools.html","",""],["Bio::DB::SAM::Tools::Bam1CoreT","","Bio/DB/SAM/Tools/Bam1CoreT.html","",""],["Bio::DB::SAM::Tools::Bam1T","","Bio/DB/SAM/Tools/Bam1T.html","",""],["Bio::DB::SAM::Tools::BamHeaderT","","Bio/DB/SAM/Tools/BamHeaderT.html","","<p>typedef struct {\n\n<pre>int32_t n_targets;\nchar **target_name;\nuint32_t *target_len;\nvoid *dict, *hash, *rg2lib; ...</pre>\n"],["Bio::DB::SAM::Tools::BamPileup1T","","Bio/DB/SAM/Tools/BamPileup1T.html","",""],["Bio::DB::SAM::Tools::SamfileT","","Bio/DB/SAM/Tools/SamfileT.html","","<p>typedef struct {\n\n<pre>int type;\nunion {\n        tamFile tamr;\n        bamFile bam;\n        FILE *tamw;\n} x; ...</pre>\n"],["Bio::DB::SAM::Tools::SamfileTX","","Bio/DB/SAM/Tools/SamfileTX.html","",""],["Bio::DB::SAMException","","Bio/DB/SAMException.html","",""],["Bio::DB::Sam","","Bio/DB/Sam.html","",""],["Bio::DB::Tag","","Bio/DB/Tag.html","",""],["LibC","","LibC.html","",""],["Pileup","","Pileup.html","","<p>Pileup \n<p>A class representing information in SAMTools pileup format\n<p>Author &mdash; Dan MacLean (dan.maclean@tsl …\n"],["Vcf","","Vcf.html","","<p>Vcf \n<p>A class representing information in Variant Call Format Forked from vcfruby\nat github.com/jesserod/vcfruby …\n"],["average_coverage","Bio::DB::Sam","Bio/DB/Sam.html#method-i-average_coverage","(chromosome, qstart, len)","<p>Returns the average coverage of a region in a bam file.\n"],["bam_sort","Bio::DB::SAM::Tools","Bio/DB/SAM/Tools.html#method-c-bam_sort","(bam_filename, bam_output_prefix)",""],["chromosome_coverage","Bio::DB::Sam","Bio/DB/Sam.html#method-i-chromosome_coverage","(chromosome, qstart, len)","<p>Returns an array with the coverage at each possition in the queried region\nThis is a simple average coverage …\n"],["close","Bio::DB::Sam","Bio/DB/Sam.html#method-i-close","()","<p>Closes the sam file and destroys the C pointers using the functions\nprovided by libbam\n"],["deprecated_pileup","Bio::DB::Sam","Bio/DB/Sam.html#method-i-deprecated_pileup","( cmd )","<p>utility method that does not use the samtools API, it calls samtools\ndirectly as if on the command line …\n"],["fetch","Bio::DB::Sam","Bio/DB/Sam.html#method-i-fetch","(chromosome, qstart, qend)","<p>Returns an array of Alignments on a given region.\n"],["fetch_reference","Bio::DB::Sam","Bio/DB/Sam.html#method-i-fetch_reference","(chromosome, qstart,qend)","<p>Returns the sequence for a given region.\n"],["fetch_with_function","Bio::DB::Sam","Bio/DB/Sam.html#method-i-fetch_with_function","(chromosome, qstart, qend, function)","<p>Executes a function on each Alignment inside the queried region of the\nchromosome. The chromosome can …\n"],["filename","Bio::DB::SAM::Library","Bio/DB/SAM/Library.html#method-c-filename","()","<p>Return the path with the file name of the library for the specific\noperating system\n"],["finalize","Bio::DB::Alignment","Bio/DB/Alignment.html#method-c-finalize","(object_id)",""],["finalize","Bio::DB::Sam","Bio/DB/Sam.html#method-c-finalize","(id)","<p>Destructor method that closes the file before letting the object be garbage\ncollected.\n"],["index_stats","Bio::DB::Sam","Bio/DB/Sam.html#method-i-index_stats","()",""],["int_or_raw","Vcf","Vcf.html#method-i-int_or_raw","(x)",""],["load_index","Bio::DB::Sam","Bio/DB/Sam.html#method-i-load_index","()","<p>Loads the bam index to be used for fetching. If the index doesn’t exists\nthe index is built provided …\n"],["load_reference","Bio::DB::Sam","Bio/DB/Sam.html#method-i-load_reference","()","<p>Loads the reference file to be able to query regions of it. This requires\nthe fai index to exist in the …\n"],["merge","Bio::DB::Sam","Bio/DB/Sam.html#method-c-merge","(files, merged_file, headers, add_RG, by_qname)","<p>Merges n BAM files. This doesn’t require to create a SAM object\n<p>files &mdash; An array with the paths to the files. …\n"],["mpileup","Bio::DB::Sam","Bio/DB/Sam.html#method-i-mpileup","( opts )","<p>calls the mpileup function, opts is a hash of options identical to the\ncommand line options for mpileup. …\n"],["mpileup_plus","Bio::DB::Sam","Bio/DB/Sam.html#method-i-mpileup_plus","( opts )","<p>experimental method that spawns a samtools mpileup | bcftools view process\nand supports returning of …\n"],["new","Bio::DB::Alignment","Bio/DB/Alignment.html#method-c-new","()",""],["new","Bio::DB::SAMException","Bio/DB/SAMException.html#method-c-new","()","<p>we can add further variables to give information of the excpetion\n"],["new","Bio::DB::Sam","Bio/DB/Sam.html#method-c-new","(optsa={})","<p>To make a new sam object. Initialize expects a hash optsa with the\nfollowing elemets:\n<p>fasta &mdash; The fasta …\n"],["new","Pileup","Pileup.html#method-c-new","(pile_up_line)","<p>creates the Pileup object\n\n<pre>pile_up_line = &quot;seq2\\t151\\tG\\tG\\t36\\t0\\t99\\t12\\t...........A\\t:9&lt;;;7=&lt;&lt;&lt;&lt;&lt;&quot; ...</pre>\n"],["new","Vcf","Vcf.html#method-c-new","(line=nil, sample_names=nil)","<p>create the vcf object, use the ordered list of sample names to label\nsamples if provided [‘A’, ‘B’, ‘C’], …\n"],["non_ref_count","Pileup","Pileup.html#method-i-non_ref_count","()","<p>returns the total non-reference bases in the reads at this position\n"],["non_refs","Pileup","Pileup.html#method-i-non_refs","()","<p>Calculate the total count of each non-reference nucleotide and return a\nhash of all 4 nt counts, returns …\n"],["open","Bio::DB::Sam","Bio/DB/Sam.html#method-i-open","()","<p>Function that actually opens the sam file Throws a SAMException if the file\ncan’t be open.\n"],["parse_line","Vcf","Vcf.html#method-i-parse_line","(line, sample_names=nil)","<p>gets the info in the Vcf lines and parses the\n"],["qname","Bio::DB::SAM::Tools::Bam1T","Bio/DB/SAM/Tools/Bam1T.html#method-i-qname","()",""],["query_string","Bio::DB::Sam","Bio/DB/Sam.html#method-i-query_string","(chromosome, qstart,qend)","<p>Generates a query sting to be used by the region parser in samtools.  In\nprinciple, you shouldn’t need …\n"],["ref_count","Pileup","Pileup.html#method-i-ref_count","()","<p>returns the count of reference-bases in the reads at this position\n"],["sam=","Bio::DB::Alignment","Bio/DB/Alignment.html#method-i-sam-3D","(sam)",""],["set","Bio::DB::Alignment","Bio/DB/Alignment.html#method-i-set","(bam_alignment, header)",""],["set","Bio::DB::Tag","Bio/DB/Tag.html#method-i-set","(str)",""],["text","Bio::DB::SAM::Tools::BamHeaderT","Bio/DB/SAM/Tools/BamHeaderT.html#method-i-text","()",""],["text=","Bio::DB::SAM::Tools::BamHeaderT","Bio/DB/SAM/Tools/BamHeaderT.html#method-i-text-3D","(str)",""],["to_s","Bio::DB::Sam","Bio/DB/Sam.html#method-i-to_s","()","<p>Prints a description of the sam file in a text format containg if it is\nbinary or text, the path and …\n"],["LICENSE","","LICENSE_txt.html","","<p>Copyright © 2011 Raoul J.P. Bonnal\n<p>Permission is hereby granted, free of charge, to any person obtaining …\n"]],"searchIndex":["bio","db","alignment","sam","library","tools","bam1coret","bam1t","bamheadert","bampileup1t","samfilet","samfiletx","samexception","sam","tag","libc","pileup","vcf","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::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","libc","pileup","vcf","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()","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::samexception::new()","bio::db::sam::new()","pileup::new()","vcf::new()","pileup#non_ref_count()","pileup#non_refs()","bio::db::sam#open()","vcf#parse_line()","bio::db::sam::tools::bam1t#qname()","bio::db::sam#query_string()","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()",""]}}

data/doc/js/searcher.js

@@ -0,0 +1,228 @@
+Searcher = function(data) {
+  this.data = data;
+  this.handlers = [];
+}
+
+Searcher.prototype = new function() {
+  // search is performed in chunks of 1000 for non-blocking user input
+  var CHUNK_SIZE = 1000;
+  // do not try to find more than 100 results
+  var MAX_RESULTS = 100;
+  var huid = 1;
+  var suid = 1;
+  var runs = 0;
+
+  this.find = function(query) {
+    var queries = splitQuery(query);
+    var regexps = buildRegexps(queries);
+    var highlighters = buildHilighters(queries);
+    var state = { from: 0, pass: 0, limit: MAX_RESULTS, n: suid++};
+    var _this = this;
+
+    this.currentSuid = state.n;
+
+    if (!query) return;
+
+    var run = function() {
+      // stop current search thread if new search started
+      if (state.n != _this.currentSuid) return;
+
+      var results =
+        performSearch(_this.data, regexps, queries, highlighters, state);
+      var hasMore = (state.limit > 0 && state.pass < 4);
+
+      triggerResults.call(_this, results, !hasMore);
+      if (hasMore) {
+        setTimeout(run, 2);
+      }
+      runs++;
+    };
+    runs = 0;
+
+    // start search thread
+    run();
+  }
+
+  /*  ----- Events ------  */
+  this.ready = function(fn) {
+    fn.huid = huid;
+    this.handlers.push(fn);
+  }
+
+  /*  ----- Utilities ------  */
+  function splitQuery(query) {
+    return jQuery.grep(query.split(/(\s+|::?|\(\)?)/), function(string) {
+      return string.match(/\S/)
+    });
+  }
+
+  function buildRegexps(queries) {
+    return jQuery.map(queries, function(query) {
+      return new RegExp(query.replace(/(.)/g, '([$1])([^$1]*?)'), 'i')
+    });
+  }
+
+  function buildHilighters(queries) {
+    return jQuery.map(queries, function(query) {
+      return jQuery.map(query.split(''), function(l, i) {
+        return '\u0001$' + (i*2+1) + '\u0002$' + (i*2+2);
+      }).join('');
+    });
+  }
+
+  // function longMatchRegexp(index, longIndex, regexps) {
+  //     for (var i = regexps.length - 1; i >= 0; i--){
+  //         if (!index.match(regexps[i]) && !longIndex.match(regexps[i])) return false;
+  //     };
+  //     return true;
+  // }
+
+
+  /*  ----- Mathchers ------  */
+
+  /*
+   * This record matches if the index starts with queries[0] and the record
+   * matches all of the regexps
+   */
+  function matchPassBeginning(index, longIndex, queries, regexps) {
+    if (index.indexOf(queries[0]) != 0) return false;
+    for (var i=1, l = regexps.length; i < l; i++) {
+      if (!index.match(regexps[i]) && !longIndex.match(regexps[i]))
+        return false;
+    };
+    return true;
+  }
+
+  /*
+   * This record matches if the longIndex starts with queries[0] and the
+   * longIndex matches all of the regexps
+   */
+  function matchPassLongIndex(index, longIndex, queries, regexps) {
+    if (longIndex.indexOf(queries[0]) != 0) return false;
+    for (var i=1, l = regexps.length; i < l; i++) {
+      if (!longIndex.match(regexps[i]))
+        return false;
+    };
+    return true;
+  }
+
+  /*
+   * This record matches if the index contains queries[0] and the record
+   * matches all of the regexps
+   */
+  function matchPassContains(index, longIndex, queries, regexps) {
+    if (index.indexOf(queries[0]) == -1) return false;
+    for (var i=1, l = regexps.length; i < l; i++) {
+      if (!index.match(regexps[i]) && !longIndex.match(regexps[i]))
+        return false;
+    };
+    return true;
+  }
+
+  /*
+   * This record matches if regexps[0] matches the index and the record
+   * matches all of the regexps
+   */
+  function matchPassRegexp(index, longIndex, queries, regexps) {
+    if (!index.match(regexps[0])) return false;
+    for (var i=1, l = regexps.length; i < l; i++) {
+      if (!index.match(regexps[i]) && !longIndex.match(regexps[i]))
+        return false;
+    };
+    return true;
+  }
+
+
+  /*  ----- Highlighters ------  */
+  function highlightRegexp(info, queries, regexps, highlighters) {
+    var result = createResult(info);
+    for (var i=0, l = regexps.length; i < l; i++) {
+      result.title = result.title.replace(regexps[i], highlighters[i]);
+      result.namespace = result.namespace.replace(regexps[i], highlighters[i]);
+    };
+    return result;
+  }
+
+  function hltSubstring(string, pos, length) {
+    return string.substring(0, pos) + '\u0001' + string.substring(pos, pos + length) + '\u0002' + string.substring(pos + length);
+  }
+
+  function highlightQuery(info, queries, regexps, highlighters) {
+    var result = createResult(info);
+    var pos = 0;
+    var lcTitle = result.title.toLowerCase();
+
+    pos = lcTitle.indexOf(queries[0]);
+    if (pos != -1) {
+      result.title = hltSubstring(result.title, pos, queries[0].length);
+    }
+
+    result.namespace = result.namespace.replace(regexps[0], highlighters[0]);
+    for (var i=1, l = regexps.length; i < l; i++) {
+      result.title = result.title.replace(regexps[i], highlighters[i]);
+      result.namespace = result.namespace.replace(regexps[i], highlighters[i]);
+    };
+    return result;
+  }
+
+  function createResult(info) {
+    var result = {};
+    result.title = info[0];
+    result.namespace = info[1];
+    result.path = info[2];
+    result.params = info[3];
+    result.snippet = info[4];
+    return result;
+  }
+
+  /*  ----- Searching ------  */
+  function performSearch(data, regexps, queries, highlighters, state) {
+    var searchIndex = data.searchIndex;
+    var longSearchIndex = data.longSearchIndex;
+    var info = data.info;
+    var result = [];
+    var i = state.from;
+    var l = searchIndex.length;
+    var togo = CHUNK_SIZE;
+    var matchFunc, hltFunc;
+
+    while (state.pass < 4 && state.limit > 0 && togo > 0) {
+      if (state.pass == 0) {
+        matchFunc = matchPassBeginning;
+        hltFunc = highlightQuery;
+      } else if (state.pass == 1) {
+        matchFunc = matchPassLongIndex;
+        hltFunc = highlightQuery;
+      } else if (state.pass == 2) {
+        matchFunc = matchPassContains;
+        hltFunc = highlightQuery;
+      } else if (state.pass == 3) {
+        matchFunc = matchPassRegexp;
+        hltFunc = highlightRegexp;
+      }
+
+      for (; togo > 0 && i < l && state.limit > 0; i++, togo--) {
+        if (info[i].n == state.n) continue;
+        if (matchFunc(searchIndex[i], longSearchIndex[i], queries, regexps)) {
+          info[i].n = state.n;
+          result.push(hltFunc(info[i], queries, regexps, highlighters));
+          state.limit--;
+        }
+      };
+      if (searchIndex.length <= i) {
+        state.pass++;
+        i = state.from = 0;
+      } else {
+        state.from = i;
+      }
+    }
+    return result;
+  }
+
+  function triggerResults(results, isLast) {
+    jQuery.each(this.handlers, function(i, fn) {
+      fn.call(this, results, isLast)
+    })
+  }
+}
+

data/doc/lib/bio-samtools_rb.html

@@ -0,0 +1,115 @@
+<!DOCTYPE html>
+
+<html>
+<head>
+<meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
+
+<title>LICENSE</title>
+
+<link type="text/css" media="screen" href="../rdoc.css" rel="stylesheet">
+
+<script type="text/javascript">
+  var rdoc_rel_prefix = "../";
+</script>
+
+<script type="text/javascript" charset="utf-8" src="../js/jquery.js"></script>
+<script type="text/javascript" charset="utf-8" src="../js/navigation.js"></script>
+<script type="text/javascript" charset="utf-8" src="../js/search_index.js"></script>
+<script type="text/javascript" charset="utf-8" src="../js/search.js"></script>
+<script type="text/javascript" charset="utf-8" src="../js/searcher.js"></script>
+<script type="text/javascript" charset="utf-8" src="../js/darkfish.js"></script>
+
+
+<body class="file">
+<nav id="metadata">
+  <nav id="home-section" class="section">
+  <h3 class="section-header">
+    <a href="../index.html">Home</a>
+    <a href="../table_of_contents.html#classes">Classes</a>
+    <a href="../table_of_contents.html#methods">Methods</a>
+  </h3>
+</nav>
+
+
+  <nav id="search-section" class="section project-section" class="initially-hidden">
+  <form action="#" method="get" accept-charset="utf-8">
+    <h3 class="section-header">
+      <input type="text" name="search" placeholder="Search" id="search-field"
+             title="Type to search, Up and Down to navigate, Enter to load">
+    </h3>
+  </form>
+
+  <ul id="search-results" class="initially-hidden"></ul>
+</nav>
+
+
+  <div id="project-metadata">
+    <nav id="fileindex-section" class="section project-section">
+  <h3 class="section-header">Pages</h3>
+
+  <ul>
+  
+    <li class="file"><a href="../LICENSE_txt.html">LICENSE</a>
+  
+  </ul>
+</nav>
+
+    <nav id="classindex-section" class="section project-section">
+  <h3 class="section-header">Class and Module Index</h3>
+
+  <ul class="link-list">
+  
+    <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/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>
+  
+    <li><a href="../Bio/DB/SAM/Tools/Bam1T.html">Bio::DB::SAM::Tools::Bam1T</a>
+  
+    <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>
+  
+    <li><a href="../Bio/DB/SAMException.html">Bio::DB::SAMException</a>
+  
+    <li><a href="../Bio/DB/Sam.html">Bio::DB::Sam</a>
+  
+    <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="../Vcf.html">Vcf</a>
+  
+  </ul>
+</nav>
+
+  </div>
+</nav>
+
+<div id="documentation" class="description">
+  
+</div>
+
+
+
+<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.
+</footer>
+

data/doc/lib/bio/db/sam/bam_rb.html

@@ -0,0 +1,121 @@
+<!DOCTYPE html>
+
+<html>
+<head>
+<meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
+
+<title>LICENSE</title>
+
+<link type="text/css" media="screen" href="../../../../rdoc.css" rel="stylesheet">
+
+<script type="text/javascript">
+  var rdoc_rel_prefix = "../../../../";
+</script>
+
+<script type="text/javascript" charset="utf-8" src="../../../../js/jquery.js"></script>
+<script type="text/javascript" charset="utf-8" src="../../../../js/navigation.js"></script>
+<script type="text/javascript" charset="utf-8" src="../../../../js/search_index.js"></script>
+<script type="text/javascript" charset="utf-8" src="../../../../js/search.js"></script>
+<script type="text/javascript" charset="utf-8" src="../../../../js/searcher.js"></script>
+<script type="text/javascript" charset="utf-8" src="../../../../js/darkfish.js"></script>
+
+
+<body class="file">
+<nav id="metadata">
+  <nav id="home-section" class="section">
+  <h3 class="section-header">
+    <a href="../../../../index.html">Home</a>
+    <a href="../../../../table_of_contents.html#classes">Classes</a>
+    <a href="../../../../table_of_contents.html#methods">Methods</a>
+  </h3>
+</nav>
+
+
+  <nav id="search-section" class="section project-section" class="initially-hidden">
+  <form action="#" method="get" accept-charset="utf-8">
+    <h3 class="section-header">
+      <input type="text" name="search" placeholder="Search" id="search-field"
+             title="Type to search, Up and Down to navigate, Enter to load">
+    </h3>
+  </form>
+
+  <ul id="search-results" class="initially-hidden"></ul>
+</nav>
+
+
+  <div id="project-metadata">
+    <nav id="fileindex-section" class="section project-section">
+  <h3 class="section-header">Pages</h3>
+
+  <ul>
+  
+    <li class="file"><a href="../../../../LICENSE_txt.html">LICENSE</a>
+  
+  </ul>
+</nav>
+
+    <nav id="classindex-section" class="section project-section">
+  <h3 class="section-header">Class and Module Index</h3>
+
+  <ul class="link-list">
+  
+    <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/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>
+  
+    <li><a href="../../../../Bio/DB/SAM/Tools/Bam1T.html">Bio::DB::SAM::Tools::Bam1T</a>
+  
+    <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>
+  
+    <li><a href="../../../../Bio/DB/SAMException.html">Bio::DB::SAMException</a>
+  
+    <li><a href="../../../../Bio/DB/Sam.html">Bio::DB::Sam</a>
+  
+    <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="../../../../Vcf.html">Vcf</a>
+  
+  </ul>
+</nav>
+
+  </div>
+</nav>
+
+<div id="documentation" class="description">
+  
+<p>require ‘rubygems’ require ‘ffi’</p>
+
+<pre class="ruby"><span class="ruby-identifier">require</span> <span class="ruby-string">'bio/db/sam/faidx'</span>
+<span class="ruby-identifier">require</span> <span class="ruby-string">'bio/db/sam/sam'</span>
+</pre>
+
+</div>
+
+
+
+<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.
+</footer>
+