RubyGems - bio-samtools - Versions diffs - 0.6.2 → 2.0.3 - Mend

bio-samtools 0.6.2 → 2.0.3

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (160) hide show

checksums.yaml +4 -4
data/Gemfile +3 -2
data/README.md +4 -7
data/VERSION +1 -1
data/bio-samtools.gemspec +47 -105
data/doc/Bio.html +68 -131
data/doc/Bio/DB.html +51 -111
data/doc/Bio/DB/Alignment.html +135 -363
data/doc/Bio/DB/Pileup.html +183 -170
data/doc/Bio/DB/SAM.html +1396 -820
data/doc/Bio/DB/SAM/Library.html +73 -123
data/doc/Bio/DB/SAM/Tools.html +51 -273
data/doc/Bio/DB/Tag.html +78 -124
data/doc/Bio/DB/Vcf.html +111 -147
data/doc/LICENSE_txt.html +113 -148
data/doc/created.rid +9 -10
data/doc/fonts.css +167 -0
data/doc/fonts/Lato-Light.ttf +0 -0
data/doc/fonts/Lato-LightItalic.ttf +0 -0
data/doc/fonts/Lato-Regular.ttf +0 -0
data/doc/fonts/Lato-RegularItalic.ttf +0 -0
data/doc/fonts/SourceCodePro-Bold.ttf +0 -0
data/doc/fonts/SourceCodePro-Regular.ttf +0 -0
data/doc/images/add.png +0 -0
data/doc/images/arrow_up.png +0 -0
data/doc/images/delete.png +0 -0
data/doc/images/tag_blue.png +0 -0
data/doc/index.html +48 -54
data/doc/js/darkfish.js +9 -22
data/doc/js/search.js +20 -5
data/doc/js/search_index.js +1 -1
data/doc/rdoc.css +255 -218
data/doc/table_of_contents.html +256 -137
data/ext/Rakefile +57 -0
data/lib/bio-samtools.rb +7 -2
data/lib/bio/BIOExtensions.rb +89 -0
data/lib/bio/db/alignment.rb +59 -0
data/lib/bio/db/fastadb.rb +255 -0
data/lib/bio/db/pileup.rb +221 -172
data/lib/bio/db/sam.rb +639 -589
data/lib/bio/db/sam/{faidx.rb → faidx_old.rb} +0 -0
data/lib/bio/db/vcf.rb +69 -68
data/test/.gitignore +1 -0
data/test/{test_basic.rb → old_test_basic.rb} +33 -1
data/test/samples/small/dupes.bam +0 -0
data/test/samples/small/dupes.sam +274 -0
data/test/samples/small/map_for_reheader.sam +8 -0
data/test/samples/small/map_to_merge1.bam +0 -0
data/test/samples/small/map_to_merge1.bam.bai +0 -0
data/test/samples/small/map_to_merge1.sam +8 -0
data/test/samples/small/map_to_merge2.bam +0 -0
data/test/samples/small/map_to_merge2.bam.bai +0 -0
data/test/samples/small/map_to_merge2.sam +8 -0
data/test/samples/small/no_md.sam +8 -0
data/test/samples/small/test_chr.fasta.1.bt2 +0 -0
data/test/samples/small/test_chr.fasta.2.bt2 +0 -0
data/test/samples/small/test_chr.fasta.3.bt2 +0 -0
data/test/samples/small/test_chr.fasta.4.bt2 +0 -0
data/test/samples/small/test_chr.fasta.rev.1.bt2 +0 -0
data/test/samples/small/test_chr.fasta.rev.2.bt2 +0 -0
data/test/samples/small/test_cov.svg +273 -0
data/test/samples/small/testu.bam.bai +0 -0
data/test/svg +133 -0
data/test/test_pileup.rb +84 -0
data/test/test_sam.rb +331 -0
data/test/test_vcf.rb +11 -0
data/{doc → tutorial}/tutorial.html +0 -0
data/{doc → tutorial}/tutorial.pdf +0 -0
metadata +56 -114
data/doc/Bio/DB/SAM/Tools/Bam1CoreT.html +0 -159
data/doc/Bio/DB/SAM/Tools/Bam1T.html +0 -220
data/doc/Bio/DB/SAM/Tools/BamHeaderT.html +0 -249
data/doc/Bio/DB/SAM/Tools/BamPileup1T.html +0 -159
data/doc/Bio/DB/SAM/Tools/SamfileT.html +0 -171
data/doc/Bio/DB/SAM/Tools/SamfileTX.html +0 -159
data/doc/Bio/DB/SAMException.html +0 -205
data/doc/LibC.html +0 -155
data/doc/Pileup.html +0 -571
data/doc/Vcf.html +0 -473
data/doc/basic_styles.css +0 -31
data/doc/classes/Bio.html +0 -139
data/doc/classes/Bio/DB.html +0 -137
data/doc/classes/Bio/DB/Alignment.html +0 -441
data/doc/classes/Bio/DB/Alignment.src/M000012.html +0 -19
data/doc/classes/Bio/DB/Alignment.src/M000013.html +0 -27
data/doc/classes/Bio/DB/Alignment.src/M000014.html +0 -45
data/doc/classes/Bio/DB/Alignment.src/M000015.html +0 -40
data/doc/classes/Bio/DB/SAM.html +0 -510
data/doc/classes/Bio/DB/SAM/Library.html +0 -135
data/doc/classes/Bio/DB/SAM/Library.src/M000006.html +0 -28
data/doc/classes/Bio/DB/SAM/Tools.html +0 -278
data/doc/classes/Bio/DB/SAM/Tools.src/M000007.html +0 -20
data/doc/classes/Bio/DB/SAM/Tools/Bam1CoreT.html +0 -111
data/doc/classes/Bio/DB/SAM/Tools/Bam1T.html +0 -150
data/doc/classes/Bio/DB/SAM/Tools/Bam1T.src/M000010.html +0 -20
data/doc/classes/Bio/DB/SAM/Tools/BamHeaderT.html +0 -169
data/doc/classes/Bio/DB/SAM/Tools/BamHeaderT.src/M000008.html +0 -19
data/doc/classes/Bio/DB/SAM/Tools/BamHeaderT.src/M000009.html +0 -18
data/doc/classes/Bio/DB/SAM/Tools/BamPileup1T.html +0 -111
data/doc/classes/Bio/DB/SAM/Tools/SamfileT.html +0 -129
data/doc/classes/Bio/DB/SAM/Tools/SamfileTX.html +0 -111
data/doc/classes/Bio/DB/SAMException.html +0 -140
data/doc/classes/Bio/DB/SAMException.src/M000016.html +0 -18
data/doc/classes/Bio/DB/Sam.src/M000017.html +0 -43
data/doc/classes/Bio/DB/Sam.src/M000018.html +0 -42
data/doc/classes/Bio/DB/Sam.src/M000019.html +0 -18
data/doc/classes/Bio/DB/Sam.src/M000020.html +0 -22
data/doc/classes/Bio/DB/Sam.src/M000021.html +0 -19
data/doc/classes/Bio/DB/Sam.src/M000022.html +0 -25
data/doc/classes/Bio/DB/Sam.src/M000023.html +0 -28
data/doc/classes/Bio/DB/Sam.src/M000024.html +0 -28
data/doc/classes/Bio/DB/Sam.src/M000025.html +0 -46
data/doc/classes/Bio/DB/Sam.src/M000026.html +0 -24
data/doc/classes/Bio/DB/Sam.src/M000027.html +0 -19
data/doc/classes/Bio/DB/Sam.src/M000028.html +0 -24
data/doc/classes/Bio/DB/Sam.src/M000029.html +0 -41
data/doc/classes/Bio/DB/Sam.src/M000030.html +0 -31
data/doc/classes/Bio/DB/Sam.src/M000031.html +0 -86
data/doc/classes/Bio/DB/Sam.src/M000032.html +0 -34
data/doc/classes/Bio/DB/Tag.html +0 -160
data/doc/classes/Bio/DB/Tag.src/M000011.html +0 -21
data/doc/classes/LibC.html +0 -105
data/doc/classes/Pileup.html +0 -374
data/doc/classes/Pileup.src/M000001.html +0 -34
data/doc/classes/Pileup.src/M000002.html +0 -21
data/doc/classes/Pileup.src/M000003.html +0 -21
data/doc/classes/Pileup.src/M000004.html +0 -21
data/doc/classes/Pileup.src/M000005.html +0 -31
data/doc/files/lib/bio-samtools_rb.html +0 -109
data/doc/files/lib/bio/db/sam/bam_rb.html +0 -108
data/doc/files/lib/bio/db/sam/faidx_rb.html +0 -108
data/doc/files/lib/bio/db/sam/library_rb.html +0 -101
data/doc/files/lib/bio/db/sam/pileup_rb.html +0 -178
data/doc/files/lib/bio/db/sam/sam_rb.html +0 -113
data/doc/files/lib/bio/db/sam_rb.html +0 -111
data/doc/fr_class_index.html +0 -43
data/doc/fr_file_index.html +0 -33
data/doc/fr_method_index.html +0 -58
data/doc/lib/bio-samtools_rb.html +0 -115
data/doc/lib/bio/db/pileup_rb.html +0 -171
data/doc/lib/bio/db/sam/bam_rb.html +0 -121
data/doc/lib/bio/db/sam/faidx_rb.html +0 -117
data/doc/lib/bio/db/sam/library_rb.html +0 -115
data/doc/lib/bio/db/sam/pileup_rb.html +0 -171
data/doc/lib/bio/db/sam/sam_rb.html +0 -121
data/doc/lib/bio/db/sam/vcf_rb.html +0 -124
data/doc/lib/bio/db/sam_rb.html +0 -115
data/doc/lib/bio/db/vcf_rb.html +0 -124
data/doc/rdoc-style.css +0 -208
data/lib/bio/db/sam/bam.rb +0 -210
data/lib/bio/db/sam/sam.rb +0 -86
data/test/samples/pipe_char/test.bam +0 -0
data/test/samples/pipe_char/test.bam.bai +0 -0
data/test/samples/pipe_char/test.tam +0 -10
data/test/samples/pipe_char/test_chr.fasta +0 -1000
data/test/samples/pipe_char/test_chr.fasta.fai +0 -1
data/test/samples/small/test +0 -0
data/test/samples/small/test.bam +0 -0
data/test/samples/small/test.fa +0 -20
data/test/samples/small/test.fai +0 -0

data/doc/basic_styles.css DELETED

@@ -1,31 +0,0 @@
-/*
-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; }
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-h3 { font-size: 24px; margin: 0 0 10px 0; }
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-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;
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-td {padding: 5px;}

data/doc/classes/Bio.html DELETED

@@ -1,139 +0,0 @@
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-     PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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-<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[
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-</head>
-<body>
-    <div id="classHeader">
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-        </tr>
-        <tr class="top-aligned-row">
-            <td><strong>In:</strong></td>
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-                <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
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-                lib/bio/db/sam/library.rb
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-                <a href="../files/lib/bio/db/sam/sam_rb.html">
-                lib/bio/db/sam/sam.rb
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-                lib/bio/db/sam.rb
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-        </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 DELETED

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-  <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">
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-</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>
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-                <a href="../../files/lib/bio/db/sam_rb.html">
-                lib/bio/db/sam.rb
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-            </td>
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-        <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>

data/doc/classes/Bio/DB/Alignment.html DELETED

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-  <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[
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-  }
-  // 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::Alignment</td>
-        </tr>
-        <tr class="top-aligned-row">
-            <td><strong>In:</strong></td>
-            <td>
-                <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 id="method-list">
-      <h3 class="section-bar">Methods</h3>
-      <div class="name-list">
-      <a href="#M000013">finalize</a>&nbsp;&nbsp;
-      <a href="#M000012">new</a>&nbsp;&nbsp;
-      <a href="#M000015">sam=</a>&nbsp;&nbsp;
-      <a href="#M000014">set</a>&nbsp;&nbsp;
-      </div>
-    </div>
-  </div>
-    <!-- if includes -->
-    <div id="section">
-    <div id="attribute-list">
-      <h3 class="section-bar">Attributes</h3>
-      <div class="name-list">
-        <table>
-        <tr class="top-aligned-row context-row">
-          <td class="context-item-name">al</td>
-          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
-          <td class="context-item-desc">
-Attributes from the format
-</td>
-        </tr>
-        <tr class="top-aligned-row context-row">
-          <td class="context-item-name">calend</td>
-          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
-          <td class="context-item-desc">
-Attributes pulled with the C library
-</td>
-        </tr>
-        <tr class="top-aligned-row context-row">
-          <td class="context-item-name">cigar</td>
-          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
-          <td class="context-item-desc">
-Attributes from the format
-</td>
-        </tr>
-        <tr class="top-aligned-row context-row">
-          <td class="context-item-name">failed_quality</td>
-          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
-          <td class="context-item-desc">
-Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
-documentation) query_strand and mate_strand are true if they are forward.
-It is the opposite to the definition in the BAM format for clarity. primary
-is the negation of is_negative from the BAM format
-</td>
-        </tr>
-        <tr class="top-aligned-row context-row">
-          <td class="context-item-name">first_in_pair</td>
-          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
-          <td class="context-item-desc">
-Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
-documentation) query_strand and mate_strand are true if they are forward.
-It is the opposite to the definition in the BAM format for clarity. primary
-is the negation of is_negative from the BAM format
-</td>
-        </tr>
-        <tr class="top-aligned-row context-row">
-          <td class="context-item-name">flag</td>
-          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
-          <td class="context-item-desc">
-Attributes from the format
-</td>
-        </tr>
-        <tr class="top-aligned-row context-row">
-          <td class="context-item-name">is_duplicate</td>
-          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
-          <td class="context-item-desc">
-Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
-documentation) query_strand and mate_strand are true if they are forward.
-It is the opposite to the definition in the BAM format for clarity. primary
-is the negation of is_negative from the BAM format
-</td>
-        </tr>
-        <tr class="top-aligned-row context-row">
-          <td class="context-item-name">is_mapped</td>
-          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
-          <td class="context-item-desc">
-Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
-documentation) query_strand and mate_strand are true if they are forward.
-It is the opposite to the definition in the BAM format for clarity. primary
-is the negation of is_negative from the BAM format
-</td>
-        </tr>
-        <tr class="top-aligned-row context-row">
-          <td class="context-item-name">is_paired</td>
-          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
-          <td class="context-item-desc">
-Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
-documentation) query_strand and mate_strand are true if they are forward.
-It is the opposite to the definition in the BAM format for clarity. primary
-is the negation of is_negative from the BAM format
-</td>
-        </tr>
-        <tr class="top-aligned-row context-row">
-          <td class="context-item-name">isize</td>
-          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
-          <td class="context-item-desc">
-Attributes from the format
-</td>
-        </tr>
-        <tr class="top-aligned-row context-row">
-          <td class="context-item-name">mapq</td>
-          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
-          <td class="context-item-desc">
-Attributes from the format
-</td>
-        </tr>
-        <tr class="top-aligned-row context-row">
-          <td class="context-item-name">mate_strand</td>
-          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
-          <td class="context-item-desc">
-Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
-documentation) query_strand and mate_strand are true if they are forward.
-It is the opposite to the definition in the BAM format for clarity. primary
-is the negation of is_negative from the BAM format
-</td>
-        </tr>
-        <tr class="top-aligned-row context-row">
-          <td class="context-item-name">mate_unmapped</td>
-          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
-          <td class="context-item-desc">
-Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
-documentation) query_strand and mate_strand are true if they are forward.
-It is the opposite to the definition in the BAM format for clarity. primary
-is the negation of is_negative from the BAM format
-</td>
-        </tr>
-        <tr class="top-aligned-row context-row">
-          <td class="context-item-name">mpos</td>
-          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
-          <td class="context-item-desc">
-Attributes from the format
-</td>
-        </tr>
-        <tr class="top-aligned-row context-row">
-          <td class="context-item-name">mrnm</td>
-          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
-          <td class="context-item-desc">
-Attributes from the format
-</td>
-        </tr>
-        <tr class="top-aligned-row context-row">
-          <td class="context-item-name">pos</td>
-          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
-          <td class="context-item-desc">
-Attributes from the format
-</td>
-        </tr>
-        <tr class="top-aligned-row context-row">
-          <td class="context-item-name">primary</td>
-          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
-          <td class="context-item-desc">
-Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
-documentation) query_strand and mate_strand are true if they are forward.
-It is the opposite to the definition in the BAM format for clarity. primary
-is the negation of is_negative from the BAM format
-</td>
-        </tr>
-        <tr class="top-aligned-row context-row">
-          <td class="context-item-name">qlen</td>
-          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
-          <td class="context-item-desc">
-Attributes pulled with the C library
-</td>
-        </tr>
-        <tr class="top-aligned-row context-row">
-          <td class="context-item-name">qname</td>
-          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
-          <td class="context-item-desc">
-Attributes from the format
-</td>
-        </tr>
-        <tr class="top-aligned-row context-row">
-          <td class="context-item-name">qual</td>
-          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
-          <td class="context-item-desc">
-Attributes from the format
-</td>
-        </tr>
-        <tr class="top-aligned-row context-row">
-          <td class="context-item-name">query_strand</td>
-          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
-          <td class="context-item-desc">
-Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
-documentation) query_strand and mate_strand are true if they are forward.
-It is the opposite to the definition in the BAM format for clarity. primary
-is the negation of is_negative from the BAM format
-</td>
-        </tr>
-        <tr class="top-aligned-row context-row">
-          <td class="context-item-name">query_unmapped</td>
-          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
-          <td class="context-item-desc">
-Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
-documentation) query_strand and mate_strand are true if they are forward.
-It is the opposite to the definition in the BAM format for clarity. primary
-is the negation of is_negative from the BAM format
-</td>
-        </tr>
-        <tr class="top-aligned-row context-row">
-          <td class="context-item-name">rname</td>
-          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
-          <td class="context-item-desc">
-Attributes from the format
-</td>
-        </tr>
-        <tr class="top-aligned-row context-row">
-          <td class="context-item-name">samstr</td>
-          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
-          <td class="context-item-desc">
-Attributes from the format
-</td>
-        </tr>
-        <tr class="top-aligned-row context-row">
-          <td class="context-item-name">second_in_pair</td>
-          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
-          <td class="context-item-desc">
-Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
-documentation) query_strand and mate_strand are true if they are forward.
-It is the opposite to the definition in the BAM format for clarity. primary
-is the negation of is_negative from the BAM format
-</td>
-        </tr>
-        <tr class="top-aligned-row context-row">
-          <td class="context-item-name">seq</td>
-          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
-          <td class="context-item-desc">
-Attributes from the format
-</td>
-        </tr>
-        <tr class="top-aligned-row context-row">
-          <td class="context-item-name">tags</td>
-          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
-          <td class="context-item-desc">
-Attributes from the format
-</td>
-        </tr>
-        </table>
-      </div>
-    </div>
-    <!-- if method_list -->
-    <div id="methods">
-      <h3 class="section-bar">Public Class methods</h3>
-      <div id="method-M000013" class="method-detail">
-        <a name="M000013"></a>
-        <div class="method-heading">
-          <a href="Alignment.src/M000013.html" target="Code" class="method-signature"
-            onclick="popupCode('Alignment.src/M000013.html');return false;">
-          <span class="method-name">finalize</span><span class="method-args">(object_id)</span>
-          </a>
-        </div>
-        <div class="method-description">
-        </div>
-      </div>
-      <div id="method-M000012" class="method-detail">
-        <a name="M000012"></a>
-        <div class="method-heading">
-          <a href="Alignment.src/M000012.html" target="Code" class="method-signature"
-            onclick="popupCode('Alignment.src/M000012.html');return false;">
-          <span class="method-name">new</span><span class="method-args">()</span>
-          </a>
-        </div>
-        <div class="method-description">
-        </div>
-      </div>
-      <h3 class="section-bar">Public Instance methods</h3>
-      <div id="method-M000015" class="method-detail">
-        <a name="M000015"></a>
-        <div class="method-heading">
-          <a href="Alignment.src/M000015.html" target="Code" class="method-signature"
-            onclick="popupCode('Alignment.src/M000015.html');return false;">
-          <span class="method-name">sam=</span><span class="method-args">(sam)</span>
-          </a>
-        </div>
-        <div class="method-description">
-        </div>
-      </div>
-      <div id="method-M000014" class="method-detail">
-        <a name="M000014"></a>
-        <div class="method-heading">
-          <a href="Alignment.src/M000014.html" target="Code" class="method-signature"
-            onclick="popupCode('Alignment.src/M000014.html');return false;">
-          <span class="method-name">set</span><span class="method-args">(bam_alignment, header)</span>
-          </a>
-        </div>
-        <div class="method-description">
-        </div>
-      </div>
-    </div>
-  </div>
-<div id="validator-badges">
-  <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
-</div>
-</body>
-</html>