bio-samtools 0.6.2 → 2.0.3

data/doc/js/search_index.js

@@ -1 +1 @@
-var search_data = {"index":{"searchIndex":["bio","db","alignment","pileup","sam","library","tools","bam1coret","bam1t","bamheadert","bampileup1t","samfilet","samfiletx","samexception","sam","tag","vcf","libc","average_coverage()","bam_sort()","chromosome_coverage()","close()","deprecated_pileup()","each_reference()","fetch()","fetch_reference()","fetch_with_function()","filename()","finalize()","finalize()","genotype_list()","index_stats()","int_or_raw()","iupac_to_base()","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()","to_s()","to_vcf()","license"],"longSearchIndex":["bio","bio::db","bio::db::alignment","bio::db::pileup","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","bio::db::vcf","libc","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#each_reference()","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::pileup#genotype_list()","bio::db::sam#index_stats()","bio::db::vcf#int_or_raw()","bio::db::pileup::iupac_to_base()","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::pileup::new()","bio::db::samexception::new()","bio::db::sam::new()","bio::db::vcf::new()","bio::db::pileup#non_ref_count()","bio::db::pileup#non_refs()","bio::db::sam#open()","bio::db::vcf#parse_line()","bio::db::sam::tools::bam1t#qname()","bio::db::sam#query_string()","bio::db::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::pileup#to_s()","bio::db::sam#to_s()","bio::db::pileup#to_vcf()",""],"info":[["Bio","","Bio.html","","<p>Bio::DB::Pileup \n<p>A class representing information in SAMTools pileup format\n<p>Author &mdash; Dan MacLean (dan.maclean@tsl …\n"],["Bio::DB","","Bio/DB.html","",""],["Bio::DB::Alignment","","Bio/DB/Alignment.html","",""],["Bio::DB::Pileup","","Bio/DB/Pileup.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","",""],["Bio::DB::Vcf","","Bio/DB/Vcf.html","",""],["LibC","","LibC.html","","<p>require ‘bio/db/pileup’ require ‘bio/db/vcf’\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"],["each_reference","Bio::DB::Sam","Bio/DB/Sam.html#method-i-each_reference","()","<p>yields each reference name and its length\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"],["genotype_list","Bio::DB::Pileup","Bio/DB/Pileup.html#method-i-genotype_list","()",""],["index_stats","Bio::DB::Sam","Bio/DB/Sam.html#method-i-index_stats","()",""],["int_or_raw","Bio::DB::Vcf","Bio/DB/Vcf.html#method-i-int_or_raw","(x)",""],["iupac_to_base","Bio::DB::Pileup","Bio/DB/Pileup.html#method-c-iupac_to_base","(alt_base)","<p>returns\n"],["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::Pileup","Bio/DB/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","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","Bio::DB::Vcf","Bio/DB/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","Bio::DB::Pileup","Bio/DB/Pileup.html#method-i-non_ref_count","()","<p>returns the total non-reference bases in the reads at this position\n"],["non_refs","Bio::DB::Pileup","Bio/DB/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","Bio::DB::Vcf","Bio/DB/Vcf.html#method-i-parse_line","(line, sample_names=nil)","<p>gets the info in the Vcf lines and parses it, setting the attributes\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","Bio::DB::Pileup","Bio/DB/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::Pileup","Bio/DB/Pileup.html#method-i-to_s","()","<p>returns pileup format line as\n"],["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"],["to_vcf","Bio::DB::Pileup","Bio/DB/Pileup.html#method-i-to_vcf","()","<p>returns basic VCF string as per samtools/misc sam2vcf.pl except that it\nscrimps on the ref for indels, …\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"]]}}
+var search_data = {"index":{"searchIndex":["bio","db","alignment","pileup","sam","library","tools","sam","tag","vcf","average_coverage()","calmd()","cat()","chromosome_coverage()","depth()","docs()","faidx()","fetch()","fetch_reference()","fetch_with_function()","filename()","fix_mates()","fixmate()","flag_stats()","flagstat()","genotype_list()","idxstats()","index()","index_stats()","int_or_raw()","iupac_to_base()","merge()","mpileup()","new()","new()","new()","new()","non_ref_count()","non_refs()","open()","parse_indel()","parse_line()","phase()","plot_chromosome_coverage()","ref_count()","reheader()","remove_duplicates()","rmdup()","set()","sort()","targetcut()","to_s()","to_vcf()","tview()","view()","license"],"longSearchIndex":["bio","bio::db","bio::db::alignment","bio::db::pileup","bio::db::sam","bio::db::sam::library","bio::db::sam::tools","bio::db::sam","bio::db::tag","bio::db::vcf","bio::db::sam#average_coverage()","bio::db::sam#calmd()","bio::db::sam#cat()","bio::db::sam#chromosome_coverage()","bio::db::sam#depth()","bio::db::sam::docs()","bio::db::sam#faidx()","bio::db::sam#fetch()","bio::db::sam#fetch_reference()","bio::db::sam#fetch_with_function()","bio::db::sam::library::filename()","bio::db::sam#fix_mates()","bio::db::sam#fixmate()","bio::db::sam#flag_stats()","bio::db::sam#flagstat()","bio::db::pileup#genotype_list()","bio::db::sam#idxstats()","bio::db::sam#index()","bio::db::sam#index_stats()","bio::db::vcf#int_or_raw()","bio::db::pileup::iupac_to_base()","bio::db::sam#merge()","bio::db::sam#mpileup()","bio::db::alignment::new()","bio::db::pileup::new()","bio::db::sam::new()","bio::db::vcf::new()","bio::db::pileup#non_ref_count()","bio::db::pileup#non_refs()","bio::db::sam#open()","bio::db::pileup#parse_indel()","bio::db::vcf#parse_line()","bio::db::sam#phase()","bio::db::sam#plot_chromosome_coverage()","bio::db::pileup#ref_count()","bio::db::sam#reheader()","bio::db::sam#remove_duplicates()","bio::db::sam#rmdup()","bio::db::tag#set()","bio::db::sam#sort()","bio::db::sam#targetcut()","bio::db::pileup#to_s()","bio::db::pileup#to_vcf()","bio::db::sam#tview()","bio::db::sam#view()",""],"info":[["Bio","","Bio.html","","<p>Bio::DB::Pileup \n<p>A class representing information in SAMTools pileup format\n<p>Author &mdash; Dan MacLean (dan.maclean@tsl.ac.uk) …\n"],["Bio::DB","","Bio/DB.html","",""],["Bio::DB::Alignment","","Bio/DB/Alignment.html","","<p>Attrobites frp, the flag field (see chapter 2.2.2 of the sam file\ndocumentation) query_strand and mate_strand …\n"],["Bio::DB::Pileup","","Bio/DB/Pileup.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","","Bio/DB/Sam.html","",""],["Bio::DB::Tag","","Bio/DB/Tag.html","","<p>a class to represent the SAM OPT values, presented in SAM as\nTAG:VTYPE:VALUE\n"],["Bio::DB::Vcf","","Bio/DB/Vcf.html","",""],["average_coverage","Bio::DB::Sam","Bio/DB/Sam.html#method-i-average_coverage","(chr,start,length)","<p>returns the average coverage over the region queried\n<p>chr - the reference name\n<p>start - the start position …\n"],["calmd","Bio::DB::Sam","Bio/DB/Sam.html#method-i-calmd","(opts={}, &block)","<p>Generate the MD tag. If the MD tag is already present, this command will\ngive a warning if the MD tag …\n"],["cat","Bio::DB::Sam","Bio/DB/Sam.html#method-i-cat","(opts={})","<p>Concatenate BAMs. The sequence dictionary of each input BAM must be\nidentical.\n<p>h - header.sam\n<p>out -[FILE] …\n"],["chromosome_coverage","Bio::DB::Sam","Bio/DB/Sam.html#method-i-chromosome_coverage","(chr,start,length)","<p>returns an array of coverage for each location for which there are mapped\nreads\n<p>chr - the reference name …\n"],["depth","Bio::DB::Sam","Bio/DB/Sam.html#method-i-depth","(opts={})","<p>returns an array for each position with [sequence_name, position, depth]\n<p>b - list of positions or regions …\n"],["docs","Bio::DB::Sam","Bio/DB/Sam.html#method-c-docs","(program, command)","<p>program  - one of &#39;samtools&#39; &#39;bcftools&#39;\n<p>command - one of the commands relevant to the …\n\n"],["faidx","Bio::DB::Sam","Bio/DB/Sam.html#method-i-faidx","(opts={})","<p>Index reference sequence in the FASTA format or extract subsequence from\nindexed reference sequence. …\n"],["fetch","Bio::DB::Sam","Bio/DB/Sam.html#method-i-fetch","(chr, start,stop, &block)","<p>fetches a subsequence and calls code block\n<p>chr - the reference name for the subsequence\n<p>start - the start …\n"],["fetch_reference","Bio::DB::Sam","Bio/DB/Sam.html#method-i-fetch_reference","(chr,start,stop, opts={:as_bio => false})","<p>fetches a subsequence from a reference genome and option returns it as a\nBio::Sequence::NA object\n<p>chr …\n"],["fetch_with_function","Bio::DB::Sam","Bio/DB/Sam.html#method-i-fetch_with_function","(chr, start,stop, &block)",""],["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"],["fix_mates","Bio::DB::Sam","Bio/DB/Sam.html#method-i-fix_mates","(opts={})","<p>Fill in mate coordinates, ISIZE and mate related flags from a name-sorted\nalignment\n<p>out_bam name of outfile …\n"],["fixmate","Bio::DB::Sam","Bio/DB/Sam.html#method-i-fixmate","(opts={})",""],["flag_stats","Bio::DB::Sam","Bio/DB/Sam.html#method-i-flag_stats","(opts={})","<p>generate simple stats with regard to the number and pairing of reads mapped\nto a reference\n"],["flagstat","Bio::DB::Sam","Bio/DB/Sam.html#method-i-flagstat","(opts={})",""],["genotype_list","Bio::DB::Pileup","Bio/DB/Pileup.html#method-i-genotype_list","()","<p>identifies the reference base and returns the indel or snp genotype as\napplicable\n"],["idxstats","Bio::DB::Sam","Bio/DB/Sam.html#method-i-idxstats","()",""],["index","Bio::DB::Sam","Bio/DB/Sam.html#method-i-index","(opts={})","<p>Index sorted alignment for fast random access. Index file\n&lt;aln.bam&gt;.bai will be created of no  …\n"],["index_stats","Bio::DB::Sam","Bio/DB/Sam.html#method-i-index_stats","()","<p>Retrieve and print stats in the index file. The output is TAB delimited\nwith each line consisting of …\n"],["int_or_raw","Bio::DB::Vcf","Bio/DB/Vcf.html#method-i-int_or_raw","(x)","<p>tests if the current variable is an Integer\n<p>x - any variable\n\n"],["iupac_to_base","Bio::DB::Pileup","Bio/DB/Pileup.html#method-c-iupac_to_base","(alt_base)","<p>returns the two bases for the corresponding iupac code\n"],["merge","Bio::DB::Sam","Bio/DB/Sam.html#method-i-merge","(opts={})","<p>Merge multiple sorted alignments\n<p>n - sort by read names\n<p>r - attach RG tag (inferred from file names)\n"],["mpileup","Bio::DB::Sam","Bio/DB/Sam.html#method-i-mpileup","(opts={}, &block)","<p>returns a Bio::DB::Pileup or Bio::DB::VCF object\n<p>region - Only generate pileup in region [chrom:start-stop] …\n"],["new","Bio::DB::Alignment","Bio/DB/Alignment.html#method-c-new","(sam_string)","<p>parses the SAM string into its constituents and set its attributes\n"],["new","Bio::DB::Pileup","Bio/DB/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","Bio::DB::Sam","Bio/DB/Sam.html#method-c-new","(args)","<p>Creates a new Bio::DB::Sam object\n<p>fasta [String] - the path to the Fasta reference sequence\n<p>bam [String] …\n"],["new","Bio::DB::Vcf","Bio/DB/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 [&#39;A&#39;, …\n"],["non_ref_count","Bio::DB::Pileup","Bio/DB/Pileup.html#method-i-non_ref_count","()","<p>returns the total non-reference bases in the reads at this position\n"],["non_refs","Bio::DB::Pileup","Bio/DB/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>backward compatibility method, returns true if file exists otherwise,\ncomplains and quits.\n"],["parse_indel","Bio::DB::Pileup","Bio/DB/Pileup.html#method-i-parse_indel","(alt)","<p>identifies if the indel is an insertion or a deletion\n"],["parse_line","Bio::DB::Vcf","Bio/DB/Vcf.html#method-i-parse_line","(line, sample_names=nil)","<p>gets the info in the Vcf lines and parses it, setting the attributes\n"],["phase","Bio::DB::Sam","Bio/DB/Sam.html#method-i-phase","(opts={})","<p>Call and phase heterozygous SNPs\n<p>A - Drop reads with ambiguous phase.\n<p>b - [STR] Prefix of BAM output.  …\n"],["plot_chromosome_coverage","Bio::DB::Sam","Bio/DB/Sam.html#method-i-plot_chromosome_coverage","(chr,start,length, opts={})","<p>returns an array of coverage for each location for which there are mapped\nreads\n<p>chr - the reference name …\n"],["ref_count","Bio::DB::Pileup","Bio/DB/Pileup.html#method-i-ref_count","()","<p>returns the count of reference-bases in the reads at this position\n"],["reheader","Bio::DB::Sam","Bio/DB/Sam.html#method-i-reheader","(header_sam, opts={})","<p>Replace the header of the current bam file with the header in header_sam\n<p>header_sam - the sam file from …\n"],["remove_duplicates","Bio::DB::Sam","Bio/DB/Sam.html#method-i-remove_duplicates","(opts={})","<p>Remove potential PCR duplicates: if multiple read pairs have identical\nexternal coordinates, only retain …\n"],["rmdup","Bio::DB::Sam","Bio/DB/Sam.html#method-i-rmdup","(opts={})",""],["set","Bio::DB::Tag","Bio/DB/Tag.html#method-i-set","(str)",""],["sort","Bio::DB::Sam","Bio/DB/Sam.html#method-i-sort","(opts={})","<p>Sort alignments by leftmost coordinates\n<p>n - sort by read name\n<p>f - use &lt;out.prefix&gt; as full file name …\n"],["targetcut","Bio::DB::Sam","Bio/DB/Sam.html#method-i-targetcut","(opts={})","<p>Identifies target regions by examining the continuity of read depth,\ncomputes haploid consensus sequences …\n"],["to_s","Bio::DB::Pileup","Bio/DB/Pileup.html#method-i-to_s","()","<p>returns pileup format line\n"],["to_vcf","Bio::DB::Pileup","Bio/DB/Pileup.html#method-i-to_vcf","()","<p>returns basic VCF string as per samtools/misc sam2vcf.pl except that it\nscrimps on the ref for indels, …\n"],["tview","Bio::DB::Sam","Bio/DB/Sam.html#method-i-tview","(opts={})","<p>used to generate a text alignment viewer\n<p>d - display, output as (H)tml or (C)urses or (T)ext\n<p>p - [chr:pos] …\n"],["view","Bio::DB::Sam","Bio/DB/Sam.html#method-i-view","(opts={},&block)","<p>runs the samtools view command\n<p>b - output BAM\n<p>h - print header for the SAM output\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"]]}}

data/doc/rdoc.css

@@ -6,40 +6,52 @@
  *
  */
 
+/* vim: ft=css et sw=2 ts=2 sts=2 */
 /* Base Green is: #6C8C22 */
 
 * { padding: 0; margin: 0; }
 
 body {
-  background: #efefef;
-  font: 14px "Helvetica Neue", Helvetica, Tahoma, sans-serif;
-  margin-left: 40px;
+  background: #fafafa;
+  font-family: Lato, sans-serif;
+  font-weight: 300;
 }
-body.file-popup {
-  font-size: 90%;
-  margin-left: 0;
+
+h1 span,
+h2 span,
+h3 span,
+h4 span,
+h5 span,
+h6 span {
+  display: none;
+  padding-left: 1em;
+  font-size: 10px;
+  vertical-align: super;
 }
 
-h1 {
-  font-size: 300%;
-  text-shadow: rgba(135,145,135,0.65) 2px 2px 3px;
-  color: #6C8C22;
+h1:hover span,
+h2:hover span,
+h3:hover span,
+h4:hover span,
+h5:hover span,
+h6:hover span {
+  display: inline;
 }
-h2,h3,h4 { margin-top: 1.5em; }
 
 :link,
 :visited {
   color: #6C8C22;
   text-decoration: none;
 }
+
 :link:hover,
 :visited:hover {
   border-bottom: 1px dotted #6C8C22;
 }
 
+code,
 pre {
-  background: #ddd;
-  padding: 0.5em 0;
+  font-family: "Source Code Pro", Monaco, monospace;
 }
 
 /* @group Generic Classes */
@@ -50,10 +62,13 @@ pre {
 
 #search-field {
   width: 98%;
-  background: #eee;
+  background: white;
   border: none;
   height: 1.5em;
   -webkit-border-radius: 4px;
+  -moz-border-radius: 4px;
+  border-radius: 4px;
+  text-align: left;
 }
 #search-field:focus {
   background: #f1edba;
@@ -89,44 +104,31 @@ pre {
 /* @end */
 
 /* @group Index Page, Standalone file pages */
-.indexpage ul {
-  line-height: 160%;
+.table-of-contents ul {
+  margin: 1em;
   list-style: none;
 }
-.indexpage ul :link,
-.indexpage ul :visited {
-  font-size: 16px;
-}
 
-.indexpage li {
-  padding-left: 20px;
+.table-of-contents ul ul {
+  margin-top: 0.25em;
 }
 
-.indexpage ul > li {
-  background: url(images/bullet_black.png) no-repeat left 4px;
-}
-.indexpage li.method {
-  background: url(images/plugin.png) no-repeat left 4px;
-}
-.indexpage li.module {
-  background: url(images/package.png) no-repeat left 4px;
-}
-.indexpage li.class {
-  background: url(images/ruby.png) no-repeat left 4px;
-}
-.indexpage li.file {
-  background: url(images/page_white_text.png) no-repeat left 4px;
+.table-of-contents ul :link,
+.table-of-contents ul :visited {
+  font-size: 16px;
 }
-.indexpage li li {
-  background: url(images/tag_blue.png) no-repeat left 4px;
+
+.table-of-contents li {
+  margin-bottom: 0.25em;
 }
-.indexpage li .toc-toggle {
+
+.table-of-contents li .toc-toggle {
   width: 16px;
   height: 16px;
   background: url(images/add.png) no-repeat;
 }
 
-.indexpage li .toc-toggle.open {
+.table-of-contents li .toc-toggle.open {
   background: url(images/delete.png) no-repeat;
 }
 
@@ -134,14 +136,32 @@ pre {
 
 /* @group Top-Level Structure */
 
-#metadata {
+nav {
   float: left;
   width: 260px;
+  font-family: Helvetica, sans-serif;
+  font-size: 14px;
 }
 
-#documentation {
-  margin: 2em 1em 5em 300px;
+main {
+  display: block;
+  margin: 0 2em 5em 260px;
+  padding-left: 20px;
   min-width: 340px;
+  font-size: 16px;
+}
+
+main h1,
+main h2,
+main h3,
+main h4,
+main h5,
+main h6 {
+  font-family: Helvetica, sans-serif;
+}
+
+.table-of-contents main {
+  margin-left: 2em;
 }
 
 #validator-badges {
@@ -152,58 +172,76 @@ pre {
 
 /* @end */
 
-/* @group Metadata Section */
-#metadata .section {
-  background-color: #dedede;
-  -moz-border-radius: 5px;
-  -webkit-border-radius: 5px;
-  border: 1px solid #aaa;
-  margin: 0 8px 8px;
+/* @group navigation */
+nav {
+  margin-bottom: 1em;
+}
+
+nav .nav-section {
+  margin-top: 2em;
+  border-top: 2px solid #aaa;
   font-size: 90%;
   overflow: hidden;
 }
-#metadata h3.section-header {
+
+nav h2 {
   margin: 0;
-  padding: 2px 8px;
-  background: #ccc;
-  color: #666;
-  -moz-border-radius-topleft: 4px;
-  -moz-border-radius-topright: 4px;
-  -webkit-border-top-left-radius: 4px;
-  -webkit-border-top-right-radius: 4px;
-  border-bottom: 1px solid #aaa;
+  padding: 2px 8px 2px 8px;
+  background-color: #e8e8e8;
+  color: #555;
+  font-size: 125%;
+  text-align: center;
 }
-#metadata #home-section h3.section-header {
-  border-bottom: 0;
+
+nav h3,
+#table-of-contents-navigation {
+  margin: 0;
+  padding: 2px 8px 2px 8px;
+  text-align: right;
+  background-color: #e8e8e8;
+  color: #555;
 }
 
-#metadata ul,
-#metadata dl,
-#metadata p {
-  padding:  8px;
+nav ul,
+nav dl,
+nav p {
+  padding: 4px 8px 0;
   list-style: none;
 }
 
-#file-metadata {
-  margin-top: 2em;
+#project-navigation .nav-section {
+  margin: 0;
+  border-top: 0;
 }
 
-#file-metadata ul {
-  padding-left: 28px;
-  list-style-image: url(images/page_green.png);
+#home-section h2 {
+  text-align: center;
 }
 
-dl.svninfo {
-  color: #666;
-  margin: 0;
-}
-dl.svninfo dt {
+#table-of-contents-navigation {
+  font-size: 1.2em;
   font-weight: bold;
+  text-align: center;
+}
+
+#search-section {
+  margin-top: 0;
+  border-top: 0;
+}
+
+#search-field-wrapper {
+  border-top: 1px solid #aaa;
+  border-bottom: 1px solid #aaa;
+  padding: 3px 8px;
+  background-color: #e8e8e8;
+  color: #555;
 }
 
 ul.link-list li {
   white-space: nowrap;
+  line-height: 1.4em;
 }
+
 ul.link-list .type {
   font-size: 8px;
   text-transform: uppercase;
@@ -213,102 +251,125 @@ ul.link-list .type {
   -webkit-border-radius: 5px;
 }
 
+.calls-super {
+  background: url(images/arrow_up.png) no-repeat right center;
+}
+
 /* @end */
 
-/* @group Class Metadata Section */
-#class-metadata {
-  margin-top: 2em;
+/* @group Documentation Section */
+main {
+  color: #333;
 }
-/* @end */
 
-/* @group Project Metadata Section */
-#project-metadata {
-  margin-top: 2em;
+main > h1:first-child,
+main > h2:first-child,
+main > h3:first-child,
+main > h4:first-child,
+main > h5:first-child,
+main > h6:first-child {
+  margin-top: 0px;
 }
 
-#project-metadata .section {
-  border: 1px solid #aaa;
+main sup {
+  vertical-align: super;
+  font-size: 0.8em;
 }
-#project-metadata h3.section-header {
-  border-bottom: 1px solid #aaa;
-  position: relative;
+
+/* The heading with the class name */
+main h1[class] {
+  margin-top: 0;
+  margin-bottom: 1em;
+  font-size: 2em;
+  color: #6C8C22;
 }
 
-#project-metadata form {
-  color: #777;
-  background: #ccc;
+main h1 {
+  margin: 2em 0 0.5em;
+  font-size: 1.7em;
 }
 
-/* @end */
+main h2 {
+  margin: 2em 0 0.5em;
+  font-size: 1.5em;
+}
 
-/* @group Documentation Section */
-.description {
-  font-size: 100%;
-  color: #333;
+main h3 {
+  margin: 2em 0 0.5em;
+  font-size: 1.2em;
 }
 
-.description p {
-  margin: 1em 0.4em;
+main h4 {
+  margin: 2em 0 0.5em;
+  font-size: 1.1em;
 }
 
-.description li p {
-  margin: 0;
+main h5 {
+  margin: 2em 0 0.5em;
+  font-size: 1em;
 }
 
-.description ol,
-.description ul {
-  margin-left: 1.5em;
+main h6 {
+  margin: 2em 0 0.5em;
+  font-size: 1em;
 }
-.description ol li,
-.description ul li {
+
+main p {
+  margin: 0 0 0.5em;
   line-height: 1.4em;
 }
 
-.note-list {
-  margin: 8px 0;
+main pre {
+  margin: 1.2em 0.5em;
+  padding: 1em;
+  font-size: 0.8em;
 }
 
-.label-list {
-  margin: 8px 1.5em;
-  border: 1px solid #ccc;
+main hr {
+  margin: 1.5em 1em;
+  border: 2px solid #ddd;
 }
-.description .label-list {
-  font-size: 14px;
+
+main blockquote {
+  margin: 0 2em 1.2em 1.2em;
+  padding-left: 0.5em;
+  border-left: 2px solid #ddd;
 }
 
-.note-list dt {
-  font-weight: bold;
+main ol,
+main ul {
+  margin: 1em 2em;
 }
-.note-list dd {
-  padding: 0 12px;
+
+main li > p {
+  margin-bottom: 0.5em;
 }
 
-.label-list dt {
-  padding: 2px 4px;
-  font-weight: bold;
-  background: #ddd;
+main dl {
+  margin: 1em 0.5em;
 }
-.label-list dd {
-  padding: 2px 12px;
+
+main dt {
+  margin-bottom: 0.5em;
+  font-weight: bold;
 }
-.label-list dd + dt,
-.note-list dd + dt {
-  margin-top: 0.7em;
+
+main dd {
+  margin: 0 1em 1em 0.5em;
 }
 
-#documentation .section {
-  font-size: 90%;
+main header h2 {
+  margin-top: 2em;
+  border-width: 0;
+  border-top: 4px solid #bbb;
+  font-size: 130%;
 }
 
-#documentation h2.section-header {
-  margin-top: 1em;
-  padding: 0.25em 0.5em;
-  background: #ccc;
-  color: #333;
-  font-size: 175%;
-  border: 1px solid #bbb;
-  -moz-border-radius: 3px;
-  -webkit-border-radius: 3px;
+main header h3 {
+  margin: 2em 0 1.5em;
+  border-width: 0;
+  border-top: 3px solid #bbb;
+  font-size: 120%;
 }
 
 .documentation-section-title {
@@ -317,47 +378,35 @@ ul.link-list .type {
 .documentation-section-title .section-click-top {
   position: absolute;
   top: 6px;
-  right: 12px;
+  left: 12px;
   font-size: 10px;
   color: #9b9877;
   visibility: hidden;
-  padding-right: 0.5px;
+  padding-left: 0.5px;
 }
 
 .documentation-section-title:hover .section-click-top {
   visibility: visible;
 }
 
-#documentation h3.section-header {
-  margin-top: 1em;
-  padding: 0.25em 0.5em;
-  background-color: #dedede;
-  color: #333;
-  font-size: 150%;
-  border: 1px solid #bbb;
-  -moz-border-radius: 3px;
-  -webkit-border-radius: 3px;
-}
-
-#constants-list > dl,
-#attributes-list > dl {
+.constants-list > dl {
   margin: 1em 0 2em;
   border: 0;
 }
-#constants-list > dl dt,
-#attributes-list > dl dt {
+
+.constants-list > dl dt {
+  margin-bottom: 0.75em;
   padding-left: 0;
-  font-weight: bold;
-  font-family: Monaco, "Andale Mono";
-  background: inherit;
+  font-family: "Source Code Pro", Monaco, monospace;
+  font-size: 110%;
 }
-#constants-list > dl dt a,
-#attributes-list > dl dt a {
+
+.constants-list > dl dt a {
   color: inherit;
 }
-#constants-list > dl dd,
-#attributes-list > dl dd {
-  margin: 0 0 1em 0;
+
+.constants-list > dl dd {
+  margin: 0 0 2em 0;
   padding: 0;
   color: #666;
 }
@@ -381,88 +430,77 @@ ul.link-list .type {
 
 /* @group Method Details */
 
-#documentation .method-source-code {
+main .method-source-code {
   display: none;
 }
 
-#documentation .method-detail {
-  margin: 0.5em 0;
-  padding: 0.5em 0;
+main .method-description .method-calls-super {
+  color: #333;
+  font-weight: bold;
+}
+
+main .method-detail {
+  margin-bottom: 2.5em;
   cursor: pointer;
 }
-#documentation .method-detail:hover {
-  background-color: #f1edba;
+
+main .method-detail:target {
+  margin-left: -10px;
+  border-left: 10px solid #f1edba;
 }
-#documentation .method-heading {
+
+main .method-heading {
   position: relative;
-  padding: 2px 4px 0 20px;
-  font-size: 125%;
+  font-family: "Source Code Pro", Monaco, monospace;
+  font-size: 110%;
   font-weight: bold;
   color: #333;
-  background: url(images/brick.png) no-repeat left bottom;
 }
-#documentation .method-heading :link,
-#documentation .method-heading :visited {
+main .method-heading :link,
+main .method-heading :visited {
   color: inherit;
 }
-#documentation .method-click-advice {
+main .method-click-advice {
   position: absolute;
   top: 2px;
   right: 5px;
-  font-size: 10px;
+  font-size: 12px;
   color: #9b9877;
   visibility: hidden;
   padding-right: 20px;
   line-height: 20px;
   background: url(images/zoom.png) no-repeat right top;
 }
-#documentation .method-heading:hover .method-click-advice {
+main .method-heading:hover .method-click-advice {
   visibility: visible;
 }
 
-#documentation .method-alias .method-heading {
-  color: #666;
-  background: url(images/brick_link.png) no-repeat left bottom;
-}
-
-#documentation .method-description,
-#documentation .aliases {
-  margin: 0 20px;
+main .method-alias .method-heading {
   color: #666;
 }
 
-#documentation .method-description p,
-#documentation .aliases p {
-  line-height: 1.2em;
+main .method-description,
+main .aliases {
+  margin-top: 0.75em;
+  color: #333;
 }
 
-#documentation .aliases {
+main .aliases {
   padding-top: 4px;
   font-style: italic;
   cursor: default;
 }
-#documentation .method-description p {
-  margin-bottom: 0.5em;
-}
-#documentation .method-description ul {
+main .method-description ul {
   margin-left: 1.5em;
 }
-pre {
-  margin: 0.5em 0;
-}
 
-#documentation .attribute-method-heading {
-  background: url(images/tag_green.png) no-repeat left bottom;
-}
-#documentation #attribute-method-details .method-detail:hover {
+main #attribute-method-details .method-detail:hover {
   background-color: transparent;
   cursor: default;
 }
-#documentation .attribute-access-type {
-  font-size: 60%;
+main .attribute-access-type {
   text-transform: uppercase;
-  vertical-align: super;
-  padding: 0 2px;
+  padding: 0 1em;
 }
 /* @end */
 
@@ -471,15 +509,12 @@ pre {
 /* @group Source Code */
 
 pre {
-  overflow: auto;
-  background: #262626;
-  color: white;
+  margin: 0.5em 0;
   border: 1px dashed #999;
   padding: 0.5em;
-}
-
-.description pre {
-  margin: 0 0.4em;
+  background: #262626;
+  color: white;
+  overflow: auto;
 }
 
 .ruby-constant   { color: #7fffd4; background: transparent; }
@@ -488,7 +523,7 @@ pre {
 .ruby-operator   { color: #00ffee; background: transparent; }
 .ruby-identifier { color: #ffdead; background: transparent; }
 .ruby-node       { color: #ffa07a; background: transparent; }
-.ruby-comment    { color: #dc0000; font-weight: bold; background: transparent; }
+.ruby-comment    { color: #dc0000; background: transparent; }
 .ruby-regexp     { color: #ffa07a; background: transparent; }
 .ruby-value      { color: #7fffd4; background: transparent; }
 
@@ -496,23 +531,24 @@ pre {
 
 
 /* @group search results */
-#search-results h1 {
-  font-size: 1em;
+#search-results {
+  font-family: Lato, sans-serif;
+  font-weight: 300;
+}
+
+#search-results .search-match {
+  font-family: Helvetica, sans-serif;
   font-weight: normal;
-  text-shadow: none;
 }
 
-#search-results .current {
-  background: #ccc;
+#search-results .search-selected {
+  background: #e8e8e8;
   border-bottom: 1px solid transparent;
 }
 
 #search-results li {
   list-style: none;
   border-bottom: 1px solid #aaa;
-  -moz-border-radius: 4px;
-  -webkit-border-radius: 4px;
-  border-radius: 4px;
   margin-bottom: 0.5em;
 }
 
@@ -537,6 +573,7 @@ pre {
 
 #search-results pre {
   margin: 0.5em;
+  font-family: "Source Code Pro", Monaco, monospace;
 }
 
 /* @end */