bio-samtools 0.2.5 → 0.3.0
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.
- data/README.rdoc +7 -20
- data/Rakefile +11 -0
- data/VERSION +1 -1
- data/bio-samtools.gemspec +67 -1
- data/doc/basic_styles.css +31 -0
- data/doc/classes/Bio.html +139 -0
- data/doc/classes/Bio/DB.html +137 -0
- data/doc/classes/Bio/DB/Alignment.html +441 -0
- data/doc/classes/Bio/DB/Alignment.src/M000012.html +19 -0
- data/doc/classes/Bio/DB/Alignment.src/M000013.html +27 -0
- data/doc/classes/Bio/DB/Alignment.src/M000014.html +45 -0
- data/doc/classes/Bio/DB/Alignment.src/M000015.html +40 -0
- data/doc/classes/Bio/DB/SAM.html +510 -0
- data/doc/classes/Bio/DB/SAM/Library.html +135 -0
- data/doc/classes/Bio/DB/SAM/Library.src/M000006.html +28 -0
- data/doc/classes/Bio/DB/SAM/Tools.html +278 -0
- data/doc/classes/Bio/DB/SAM/Tools.src/M000007.html +20 -0
- data/doc/classes/Bio/DB/SAM/Tools/Bam1CoreT.html +111 -0
- data/doc/classes/Bio/DB/SAM/Tools/Bam1T.html +150 -0
- data/doc/classes/Bio/DB/SAM/Tools/Bam1T.src/M000010.html +20 -0
- data/doc/classes/Bio/DB/SAM/Tools/BamHeaderT.html +169 -0
- data/doc/classes/Bio/DB/SAM/Tools/BamHeaderT.src/M000008.html +19 -0
- data/doc/classes/Bio/DB/SAM/Tools/BamHeaderT.src/M000009.html +18 -0
- data/doc/classes/Bio/DB/SAM/Tools/BamPileup1T.html +111 -0
- data/doc/classes/Bio/DB/SAM/Tools/SamfileT.html +129 -0
- data/doc/classes/Bio/DB/SAM/Tools/SamfileTX.html +111 -0
- data/doc/classes/Bio/DB/SAMException.html +140 -0
- data/doc/classes/Bio/DB/SAMException.src/M000016.html +18 -0
- data/doc/classes/Bio/DB/Sam.src/M000017.html +43 -0
- data/doc/classes/Bio/DB/Sam.src/M000018.html +42 -0
- data/doc/classes/Bio/DB/Sam.src/M000019.html +18 -0
- data/doc/classes/Bio/DB/Sam.src/M000020.html +22 -0
- data/doc/classes/Bio/DB/Sam.src/M000021.html +19 -0
- data/doc/classes/Bio/DB/Sam.src/M000022.html +25 -0
- data/doc/classes/Bio/DB/Sam.src/M000023.html +28 -0
- data/doc/classes/Bio/DB/Sam.src/M000024.html +28 -0
- data/doc/classes/Bio/DB/Sam.src/M000025.html +46 -0
- data/doc/classes/Bio/DB/Sam.src/M000026.html +24 -0
- data/doc/classes/Bio/DB/Sam.src/M000027.html +19 -0
- data/doc/classes/Bio/DB/Sam.src/M000028.html +24 -0
- data/doc/classes/Bio/DB/Sam.src/M000029.html +41 -0
- data/doc/classes/Bio/DB/Sam.src/M000030.html +31 -0
- data/doc/classes/Bio/DB/Sam.src/M000031.html +86 -0
- data/doc/classes/Bio/DB/Sam.src/M000032.html +34 -0
- data/doc/classes/Bio/DB/Tag.html +160 -0
- data/doc/classes/Bio/DB/Tag.src/M000011.html +21 -0
- data/doc/classes/LibC.html +105 -0
- data/doc/classes/Pileup.html +374 -0
- data/doc/classes/Pileup.src/M000001.html +34 -0
- data/doc/classes/Pileup.src/M000002.html +21 -0
- data/doc/classes/Pileup.src/M000003.html +21 -0
- data/doc/classes/Pileup.src/M000004.html +21 -0
- data/doc/classes/Pileup.src/M000005.html +31 -0
- data/doc/created.rid +1 -0
- data/doc/files/lib/bio-samtools_rb.html +109 -0
- data/doc/files/lib/bio/db/sam/bam_rb.html +108 -0
- data/doc/files/lib/bio/db/sam/faidx_rb.html +108 -0
- data/doc/files/lib/bio/db/sam/library_rb.html +101 -0
- data/doc/files/lib/bio/db/sam/pileup_rb.html +178 -0
- data/doc/files/lib/bio/db/sam/sam_rb.html +113 -0
- data/doc/files/lib/bio/db/sam_rb.html +111 -0
- data/doc/fr_class_index.html +43 -0
- data/doc/fr_file_index.html +33 -0
- data/doc/fr_method_index.html +58 -0
- data/doc/index.html +24 -0
- data/doc/rdoc-style.css +208 -0
- data/doc/tutorial.html +165 -0
- data/doc/tutorial.pdf +0 -0
- data/lib/bio/db/sam.rb +163 -1
- data/lib/bio/db/sam/pileup.rb +98 -0
- data/test/basictest.rb +14 -0
- data/test/pileup.rb +68 -0
- metadata +84 -18
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<td><strong>Path:</strong></td>
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<td>lib/bio/db/sam/library.rb
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<td><strong>Last Update:</strong></td>
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<td>Wed Oct 26 21:06:33 +0100 2011</td>
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<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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<title>File: pileup.rb</title>
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<h1>pileup.rb</h1>
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<td><strong>Path:</strong></td>
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<td>lib/bio/db/sam/pileup.rb
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</td>
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<td><strong>Last Update:</strong></td>
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<td>Wed Oct 26 20:44:30 +0100 2011</td>
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<div id="description">
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<h1><a href="../../../../../classes/Pileup.html">Pileup</a></h1>
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A class representing information in SAMTools pileup format
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</p>
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<table>
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<tr><td valign="top">Author:</td><td>Dan MacLean (dan.maclean@tsl.ac.uk)
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</td></tr>
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</table>
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<p>
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<a href="../../../../../classes/Pileup.html">Pileup</a> is described at <a
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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>.
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Briefly (when you invoke pileup with the -c option):
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</p>
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<ul>
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<li>1 reference sequence name
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</li>
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<li>2 reference coordinate
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<li>(3) reference base, or `*’ for an indel line
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</li>
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<li>(4) genotype where heterozygotes are encoded in the IUB code: M=A/C, R=A/G,
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W=A/T, S=C/G, Y=C/T and K=G/T; indels are indicated by, for example, */+A,
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-A/* or +CC/-C. There is no difference between */+A or +A/*.
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</li>
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<li>(5) Phred-scaled likelihood that the genotype is wrong, which is also
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called `consensus quality’.
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</li>
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<li>(6) Phred-scaled likelihood that the genotype is identical to the
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reference, which is also called `SNP quality’. Suppose the reference
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base is A and in alignment we see 17 G and 3 A. We will get a low consensus
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quality because it is difficult to distinguish an A/G heterozygote from a
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G/G homozygote. We will get a high SNP quality, though, because the
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evidence of a SNP is very strong.
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</li>
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<li>(7) root mean square (RMS) mapping quality
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</li>
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<li>8 # reads covering the position
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</li>
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<li>9 read bases at a SNP line (check the manual page for more information);
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the 1st indel allele otherwise
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</li>
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<li>10 base quality at a SNP line; the 2nd indel allele otherwise
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</li>
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<li>(11) indel line only: # reads directly supporting the 1st indel allele
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</li>
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<li>(12) indel line only: # reads directly supporting the 2nd indel allele
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</li>
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<li>(13) indel line only: # reads supporting a third indel allele
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</li>
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</ul>
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<p>
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If pileup is invoked without `-c’, indel lines and columns between 3
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and 7 inclusive will not be outputted.
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</p>
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<p>
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NB mpileup uses the 6 column output format eg
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"seq2\t151\tG\tG\t36\t0\t99\t12\t...........A\t:9<;;7=<<<<<"
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<a href="../../../../../classes/Pileup.html">Pileup</a> provides accessors
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for all columns (6 or 10 column format) and a few other useful methods
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<pre>
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sam.rb
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Created by Ricardo Ramirez on 3/25/10.
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require ‘rubygems’ require‘ffi’ require
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bio/db/sam/library
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bio/db/sam/bam
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bio/db/sam/faidx
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bio/db/sam/sam
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