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

bio-samtools 0.6.2 → 2.0.3

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/files/lib/bio/db/sam/library_rb.html DELETED

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-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
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-  <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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-      <td>lib/bio/db/sam/library.rb
-      </td>
-    </tr>
-    <tr class="top-aligned-row">
-      <td><strong>Last Update:</strong></td>
-      <td>Wed Oct 26 21:06:33 +0100 2011</td>
-    </tr>
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-</body>
-</html>

data/doc/files/lib/bio/db/sam/pileup_rb.html DELETED

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-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
-  <title>File: pileup.rb</title>
-  <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
-  <meta http-equiv="Content-Script-Type" content="text/javascript" />
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-  <div id="fileHeader">
-    <h1>pileup.rb</h1>
-    <table class="header-table">
-    <tr class="top-aligned-row">
-      <td><strong>Path:</strong></td>
-      <td>lib/bio/db/sam/pileup.rb
-      </td>
-    </tr>
-    <tr class="top-aligned-row">
-      <td><strong>Last Update:</strong></td>
-      <td>Wed Oct 26 20:44:30 +0100 2011</td>
-    </tr>
-    </table>
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-  <!-- banner header -->
-  <div id="bodyContent">
-  <div id="contextContent">
-    <div id="description">
-      <h1><a href="../../../../../classes/Pileup.html">Pileup</a></h1>
-<p>
-A class representing information in SAMTools pileup format
-</p>
-<table>
-<tr><td valign="top">Author:</td><td>Dan MacLean (dan.maclean@tsl.ac.uk)
-</td></tr>
-</table>
-<p>
-<a href="../../../../../classes/Pileup.html">Pileup</a> 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>1 reference sequence name
-</li>
-<li>2 reference coordinate
-</li>
-<li>(3) reference base, or `*&#8217; for an indel line
-</li>
-<li>(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/*.
-</li>
-<li>(5) Phred-scaled likelihood that the genotype is wrong, which is also
-called `consensus quality&#8217;.
-</li>
-<li>(6) Phred-scaled likelihood that the genotype is identical to the
-reference, which is also called `SNP quality&#8217;. 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.
-</li>
-<li>(7) root mean square (RMS) mapping quality
-</li>
-<li>8 # reads covering the position
-</li>
-<li>9 read bases at a SNP line (check the manual page for more information);
-the 1st indel allele otherwise
-</li>
-<li>10 base quality at a SNP line; the 2nd indel allele otherwise
-</li>
-<li>(11) indel line only: # reads directly supporting the 1st indel allele
-</li>
-<li>(12) indel line only: # reads directly supporting the 2nd indel allele
-</li>
-<li>(13) indel line only: # reads supporting a third indel allele
-</li>
-</ul>
-<p>
-If pileup is invoked without `-c&#8217;, indel lines and columns between 3
-and 7 inclusive will not be outputted.
-</p>
-<p>
-NB mpileup uses the 6 column output format eg
-&quot;seq2\t151\tG\tG\t36\t0\t99\t12\t...........A\t:9&lt;;;7=&lt;&lt;&lt;&lt;&lt;&quot;
-<a href="../../../../../classes/Pileup.html">Pileup</a> provides accessors
-for all columns (6 or 10 column format) and a few other useful methods
-</p>
-    </div>
-   </div>
-  </div>
-    <!-- if includes -->
-    <div id="section">
-    <!-- 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>

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-  <div id="fileHeader">
-    <h1>sam.rb</h1>
-    <table class="header-table">
-    <tr class="top-aligned-row">
-      <td><strong>Path:</strong></td>
-      <td>lib/bio/db/sam/sam.rb
-      </td>
-    </tr>
-    <tr class="top-aligned-row">
-      <td><strong>Last Update:</strong></td>
-      <td>Wed Oct 26 21:06:33 +0100 2011</td>
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-  </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">
-    <!-- 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>

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-<head>
-  <title>File: sam.rb</title>
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-    <h1>sam.rb</h1>
-    <table class="header-table">
-    <tr class="top-aligned-row">
-      <td><strong>Path:</strong></td>
-      <td>lib/bio/db/sam.rb
-      </td>
-    </tr>
-    <tr class="top-aligned-row">
-      <td><strong>Last Update:</strong></td>
-      <td>Wed Oct 26 21:32:46 +0100 2011</td>
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-  </div>
-  <!-- banner header -->
-  <div id="bodyContent">
-  <div id="contextContent">
-    <div id="requires-list">
-      <h3 class="section-bar">Required files</h3>
-      <div class="name-list">
-      bio/db/sam/library&nbsp;&nbsp;
-      bio/db/sam/bam&nbsp;&nbsp;
-      bio/db/sam/faidx&nbsp;&nbsp;
-      bio/db/sam/sam&nbsp;&nbsp;
-      </div>
-    </div>
-   </div>
-  </div>
-    <!-- if includes -->
-    <div id="section">
-    <!-- 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>