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","","

Bio::DB::Pileup \n

A class representing information in SAMTools pileup format\n

Author — Dan MacLean (dan.maclean@tsl.ac.uk) …\n"],["Bio::DB","","Bio/DB.html","",""],["Bio::DB::Alignment","","Bio/DB/Alignment.html","","

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","","

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)","

returns the average coverage over the region queried\n

chr - the reference name\n

start - the start position …\n"],["calmd","Bio::DB::Sam","Bio/DB/Sam.html#method-i-calmd","(opts={}, &block)","

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={})","

Concatenate BAMs. The sequence dictionary of each input BAM must be\nidentical.\n

h - header.sam\n

out -[FILE] …\n"],["chromosome_coverage","Bio::DB::Sam","Bio/DB/Sam.html#method-i-chromosome_coverage","(chr,start,length)","

returns an array of coverage for each location for which there are mapped\nreads\n

chr - the reference name …\n"],["depth","Bio::DB::Sam","Bio/DB/Sam.html#method-i-depth","(opts={})","

returns an array for each position with [sequence_name, position, depth]\n

b - list of positions or regions …\n"],["docs","Bio::DB::Sam","Bio/DB/Sam.html#method-c-docs","(program, command)","

program - one of 'samtools' 'bcftools'\n

command - one of the commands relevant to the …\n\n"],["faidx","Bio::DB::Sam","Bio/DB/Sam.html#method-i-faidx","(opts={})","

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)","

fetches a subsequence and calls code block\n

chr - the reference name for the subsequence\n

start - the start …\n"],["fetch_reference","Bio::DB::Sam","Bio/DB/Sam.html#method-i-fetch_reference","(chr,start,stop, opts={:as_bio => false})","

fetches a subsequence from a reference genome and option returns it as a\nBio::Sequence::NA object\n

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","()","

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={})","

Fill in mate coordinates, ISIZE and mate related flags from a name-sorted\nalignment\n

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={})","

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","()","

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={})","

Index sorted alignment for fast random access. Index file\n<aln.bam>.bai will be created of no …\n"],["index_stats","Bio::DB::Sam","Bio/DB/Sam.html#method-i-index_stats","()","

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)","

tests if the current variable is an Integer\n

x - any variable\n\n"],["iupac_to_base","Bio::DB::Pileup","Bio/DB/Pileup.html#method-c-iupac_to_base","(alt_base)","

returns the two bases for the corresponding iupac code\n"],["merge","Bio::DB::Sam","Bio/DB/Sam.html#method-i-merge","(opts={})","

Merge multiple sorted alignments\n

n - sort by read names\n

r - attach RG tag (inferred from file names)\n"],["mpileup","Bio::DB::Sam","Bio/DB/Sam.html#method-i-mpileup","(opts={}, &block)","

returns a Bio::DB::Pileup or Bio::DB::VCF object\n

region - Only generate pileup in region [chrom:start-stop] …\n"],["new","Bio::DB::Alignment","Bio/DB/Alignment.html#method-c-new","(sam_string)","

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)","

creates the Pileup object\n\n

pile_up_line = "seq2\\t151\\tG\\tG\\t36\\t0\\t99\\t12\\t...........A\\t:9<;;7=<<<<<" ...
\n"],["new","Bio::DB::Sam","Bio/DB/Sam.html#method-c-new","(args)","

Creates a new Bio::DB::Sam object\n

fasta [String] - the path to the Fasta reference sequence\n

bam [String] …\n"],["new","Bio::DB::Vcf","Bio/DB/Vcf.html#method-c-new","(line=nil, sample_names=nil)","

create the vcf object, use the ordered list of sample names to label\nsamples if provided ['A', …\n"],["non_ref_count","Bio::DB::Pileup","Bio/DB/Pileup.html#method-i-non_ref_count","()","

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","()","

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","()","

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)","

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)","

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={})","

Call and phase heterozygous SNPs\n

A - Drop reads with ambiguous phase.\n

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={})","

returns an array of coverage for each location for which there are mapped\nreads\n

chr - the reference name …\n"],["ref_count","Bio::DB::Pileup","Bio/DB/Pileup.html#method-i-ref_count","()","

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={})","

Replace the header of the current bam file with the header in header_sam\n

header_sam - the sam file from …\n"],["remove_duplicates","Bio::DB::Sam","Bio/DB/Sam.html#method-i-remove_duplicates","(opts={})","

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={})","

Sort alignments by leftmost coordinates\n

n - sort by read name\n

f - use <out.prefix> as full file name …\n"],["targetcut","Bio::DB::Sam","Bio/DB/Sam.html#method-i-targetcut","(opts={})","

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","()","

returns pileup format line\n"],["to_vcf","Bio::DB::Pileup","Bio/DB/Pileup.html#method-i-to_vcf","()","

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={})","

used to generate a text alignment viewer\n

d - display, output as (H)tml or (C)urses or (T)ext\n

p - [chr:pos] …\n"],["view","Bio::DB::Sam","Bio/DB/Sam.html#method-i-view","(opts={},&block)","

runs the samtools view command\n

b - output BAM\n

h - print header for the SAM output\n"],["LICENSE","","LICENSE_txt.html","","

Copyright © 2011 Raoul J.P. Bonnal\n

Permission is hereby granted, free of charge, to any person obtaining …\n"]]}}