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"]]}}