bio-samtools 0.2.5 → 0.3.0
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- 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
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<h1>pileup.rb</h1>
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<td>lib/bio/db/sam/pileup.rb
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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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<tr><td valign="top">Author:</td><td>Dan MacLean (dan.maclean@tsl.ac.uk)
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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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<li>(4) genotype where heterozygotes are encoded in the IUB code: M=A/C, R=A/G,
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<li>(5) Phred-scaled likelihood that the genotype is wrong, which is also
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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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<li>(7) root mean square (RMS) mapping quality
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<li>9 read bases at a SNP line (check the manual page for more information);
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<li>(11) indel line only: # reads directly supporting the 1st indel allele
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<li>(13) indel line only: # reads supporting a third indel allele
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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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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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