Package: Rsamtools 2.29.0

Bioconductor Package Maintainer

Rsamtools: Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import

This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities for manipulating SAM (Sequence Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.

Authors:Martin Morgan [aut], Hervé Pagès [aut], Valerie Obenchain [aut], Nathaniel Hayden [aut], Busayo Samuel [ctb], Bioconductor Package Maintainer [cre]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Rsamtools/json (API)

# Install 'Rsamtools' in R:

install.packages('Rsamtools', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bioconductor/rsamtools/issues

Uses libs:

curl– Easy-to-use client-side URL transfer library
bzip2– High-quality block-sorting file compressor library
xz-utils– XZ-format compression library
zlib– Compression library
c++– GNU Standard C++ Library v3

On BioConductor:Rsamtools-2.29.0(bioc 3.24)Rsamtools-2.28.0(bioc 3.23)

dataimport sequencing coverage alignment qualitycontrol bioconductor-package core-package curl bzip2 xz-utils zlib cpp

13.99 score 30 stars 611 packages 4.5k scripts 138 mentions 138 exports 20 dependencies

Last updated from:4fdb05737c. Checks:4 ERROR, 1 OK, 8 WARNING, 1 FAIL. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	604
linux-devel-arm64	ERROR	600
linux-devel-x86_64	ERROR	695
source / vignettes	OK	800
linux-release-arm64	WARNING	603
linux-release-x86_64	WARNING	798
macos-release-arm64	WARNING	307
macos-release-x86_64	WARNING	619
macos-oldrel-arm64	WARNING	265
macos-oldrel-x86_64	WARNING	411
windows-devel	ERROR	535
windows-release	WARNING	359
windows-oldrel	WARNING	445
wasm-release	FAIL	440

Exports:applyPileups ApplyPileupsParam asBam asBcf asMates asMates<-asSam bamDirname<-bamExperiment BamFile BamFileList bamFlag bamFlag<-bamFlagAND bamFlagAsBitMatrix bamFlagTest bamIndicies bamMapqFilter bamMapqFilter<-bamPaths bamRanges bamRanges<-bamReverseComplement bamReverseComplement<-BamSampler bamSamples bamSamples<-bamSimpleCigar bamSimpleCigar<-bamTag bamTag<-bamTagFilter bamTagFilter<-BamViews bamWhat bamWhat<-bamWhich bamWhich<-BcfFile BcfFileList bcfFixed bcfGeno bcfInfo bcfMode bcfSamples bcfTrimEmpty bcfWhich bgzip bgzipTabix close.BamFile close.BcfFile close.FaFile close.RsamtoolsFileList close.TabixFile countBam countFa countTabix FaFile FaFileList filterBam FLAG_BITNAMES getSeq gzindex gzindex<-headerTabix idxstatsBam index index<-indexBam indexBcf indexFa indexTabix isIncomplete isOpen mergeBam obeyQname obeyQname<-open.BamFile open.BcfFile open.FaFile open.RsamtoolsFileList open.TabixFile phred2ASCIIOffset pileup PileupFiles PileupParam plpFiles plpFlag plpFlag<-plpMaxDepth plpMaxDepth<-plpMinBaseQuality plpMinBaseQuality<-plpMinDepth plpMinDepth<-plpMinMapQuality plpMinMapQuality<-plpParam plpWhat plpWhat<-plpWhich plpWhich<-plpYieldAll plpYieldAll<-plpYieldBy plpYieldBy<-plpYieldSize plpYieldSize<-qnamePrefixEnd qnamePrefixEnd<-qnameSuffixStart qnameSuffixStart<-quickBamCounts quickBamFlagSummary quickCountBam razip readPileup scanBam scanBamFlag scanBamHeader ScanBamParam scanBamWhat scanBcf scanBcfHeader ScanBcfParam scanFa scanFaIndex scanTabix seqinfo seqnamesTabix show sortBam TabixFile TabixFileList testPairedEndBam yieldSize yieldSize<-yieldTabix

Dependencies:BH BiocGenerics BiocParallel Biostrings bitops codetools cpp11 crayon formatR futile.logger futile.options generics GenomicRanges IRanges lambda.r Rhtslib S4Vectors Seqinfo snow XVector

An Introduction to Rsamtools

Rendered fromRsamtools-Overview.Rmdusingknitr::rmarkdown

Last update: 2023-04-04
Started: 2023-04-04

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
'samtools' aligned sequence utilities interface	Rsamtools-package bzfile-class fifo-class gzfile-class pipe-class Rsamtools unz-class url-class
Apply a user-provided function to calculate pile-up statistics across multiple BAM files.	applyPileups
Parameters for creating pileups from BAM files	ApplyPileupsParam ApplyPileupsParam-class plpFlag plpFlag<- plpMaxDepth plpMaxDepth<- plpMinBaseQuality plpMinBaseQuality<- plpMinDepth plpMinDepth<- plpMinMapQuality plpMinMapQuality<- plpWhat plpWhat<- plpWhich plpWhich<- plpYieldAll plpYieldAll<- plpYieldBy plpYieldBy<- plpYieldSize plpYieldSize<- show,ApplyPileupsParam-method
Maintain and use BAM files	asMates asMates,BamFile-method asMates,BamFileList-method asMates<- asMates<-,BamFile-method asMates<-,BamFileList-method BamFile BamFile-class BamFileList BamFileList-class close.BamFile countBam,BamFile-method countBam,BamFileList-method filterBam,BamFile-method idxstatsBam,BamFile-method indexBam,BamFile-method isIncomplete,BamFile-method isOpen,BamFile-method mergeBam,BamFileList-method obeyQname obeyQname,BamFile-method obeyQname,BamFileList-method obeyQname<- obeyQname<-,BamFile-method obeyQname<-,BamFileList-method open.BamFile qnamePrefixEnd qnamePrefixEnd,BamFile-method qnamePrefixEnd,BamFileList-method qnamePrefixEnd<- qnamePrefixEnd<-,BamFile-method qnamePrefixEnd<-,BamFileList-method qnameSuffixStart qnameSuffixStart,BamFile-method qnameSuffixStart,BamFileList-method qnameSuffixStart<- qnameSuffixStart<-,BamFile-method qnameSuffixStart<-,BamFileList-method quickBamFlagSummary,BamFile-method scanBam,BamFile-method scanBamHeader,BamFile-method seqinfo,BamFile-method seqinfo,BamFileList-method show,BamFile-method show,BamFileList-method sortBam,BamFile-method
Import, count, index, filter, sort, and merge `BAM' (binary alignment) files.	asBam asBam,character-method asSam asSam,character-method countBam countBam,character-method filterBam filterBam,character-method idxstatsBam idxstatsBam,character-method indexBam indexBam,character-method mergeBam mergeBam,character-method scanBam scanBam,character-method scanBamHeader scanBamHeader,character-method sortBam sortBam,character-method
Views into a set of BAM files	bamDirname<- bamExperiment bamIndicies bamPaths bamRanges bamRanges<- bamSamples bamSamples<- BamViews BamViews,GRanges-method BamViews,missing-method BamViews-class countBam,BamViews-method dim,BamViews-method dimnames,BamViews-method dimnames<-,BamViews,ANY-method dimnames<-,BamViews-method names,BamViews-method names<-,BamViews-method scanBam,BamViews-method show,BamViews-method [,BamViews,ANY,ANY-method [,BamViews,ANY,missing-method [,BamViews,missing,ANY-method
Manipulate BCF files.	BcfFile BcfFile-class BcfFileList BcfFileList-class bcfMode close.BcfFile indexBcf,BcfFile-method isOpen,BcfFile-method open.BcfFile scanBcf,BcfFile-method scanBcfHeader,BcfFile-method
Operations on `BCF' files.	asBcf asBcf,character-method indexBcf indexBcf,character-method scanBcf scanBcf,character-method scanBcfHeader scanBcfHeader,character-method
File compression for tabix (bgzip) and fasta (razip) files. IMPORTANT NOTE: Starting with Rsamtools 1.99.0 (Bioconductor 3.9), 'razip()' is defunct. Please use 'bgzip()' instead.	bgzip razip
Deprecated functions	BamSampler BamSampler-class scanBam,BamSampler-method show,BamSampler-method yieldTabix yieldTabix,TabixFile-method
Manipulate indexed fasta files.	close.FaFile countFa,FaFile-method FaFile FaFile-class FaFileList FaFileList-class getSeq,FaFile-method getSeq,FaFileList-method gzindex gzindex,FaFile-method gzindex,FaFileList-method gzindex<- gzindex<-,FaFile-method gzindex<-,FaFileList-method indexFa,FaFile-method isOpen,FaFile-method open.FaFile scanFa,FaFile,GRanges-method scanFa,FaFile,IntegerRangesList-method scanFa,FaFile,missing-method scanFaIndex,FaFile-method scanFaIndex,FaFileList-method seqinfo,FaFile-method show,FaFile-method
Operations on indexed 'fasta' files.	countFa countFa,character-method indexFa indexFa,character-method scanFa scanFa,character,GRanges-method scanFa,character,IntegerRangesList-method scanFa,character,missing-method scanFaIndex scanFaIndex,character-method
Retrieve sequence names defined in a tabix file.	headerTabix headerTabix,character-method
Compress and index tabix-compatible files.	indexTabix
Use filters and output formats to calculate pile-up statistics for a BAM file.	cycle_bins distinguish_nucleotides distinguish_strands ignore_query_Ns include_deletions include_insertions left_bins max_depth min_base_quality min_mapq min_minor_allele_depth min_nucleotide_depth phred2ASCIIOffset pileup pileup,BamFile-method pileup,character-method PileupParam PileupParam-class query_bins show,PileupParam-method
Represent BAM files for pileup summaries.	applyPileups,PileupFiles,ApplyPileupsParam-method applyPileups,PileupFiles,missing-method isOpen,PileupFiles-method PileupFiles PileupFiles,character-method PileupFiles,list-method PileupFiles-class plpFiles plpParam show,PileupFiles-method
Group the records of a BAM file based on their flag bits and count the number of records in each group	quickBamFlagSummary quickBamFlagSummary,character-method quickBamFlagSummary,list-method
Import samtools 'pileup' files.	readPileup readPileup,character-method readPileup,connection-method
A base class for managing file references in Rsamtools	index index,RsamtoolsFile-method index<- index<-,RsamtoolsFile-method isOpen,RsamtoolsFile-method path path,RsamtoolsFile-method RsamtoolsFile RsamtoolsFile-class show,RsamtoolsFile-method yieldSize yieldSize,RsamtoolsFile-method yieldSize<- yieldSize<-,RsamtoolsFile-method
A base class for managing lists of Rsamtools file references	close.RsamtoolsFileList index,RsamtoolsFileList-method index<-,RsamtoolsFileList-method isOpen,RsamtoolsFileList-method names,RsamtoolsFileList-method open.RsamtoolsFileList path,RsamtoolsFileList-method RsamtoolsFileList RsamtoolsFileList-class yieldSize,RsamtoolsFileList-method yieldSize<-,RsamtoolsFileList-method
Parameters for scanning BAM files	bamFlag bamFlag<- bamFlagAND bamFlagAsBitMatrix bamFlagTest bamMapqFilter bamMapqFilter<- bamReverseComplement bamReverseComplement<- bamSimpleCigar bamSimpleCigar<- bamTag bamTag<- bamTagFilter bamTagFilter<- bamWhat bamWhat<- bamWhich bamWhich<- bamWhich<-,ScanBamParam,ANY-method bamWhich<-,ScanBamParam,GRanges-method bamWhich<-,ScanBamParam,IntegerRangesList-method FLAG_BITNAMES hasUnmappedMate isDuplicate isFirstMateRead isMateMinusStrand isMinusStrand isNotPassingQualityControls isNotPrimaryRead isPaired isProperPair isSecondaryAlignment isSecondMateRead isUnmappedQuery scanBamFlag ScanBamParam ScanBamParam,ANY-method ScanBamParam,GRanges-method ScanBamParam,IntegerRangesList-method ScanBamParam,missing-method ScanBamParam-class scanBamWhat show,ScanBamParam-method
Parameters for scanning BCF files	bcfFixed bcfGeno bcfInfo bcfSamples bcfTrimEmpty bcfWhich ScanBcfParam ScanBcfParam,GRanges-method ScanBcfParam,GRangesList-method ScanBcfParam,IntegerRangesList-method ScanBcfParam,missing-method ScanBcfParam-class ScanBVcfParam-class show,ScanBVcfParam-method
Retrieve sequence names defined in a tabix file.	seqnamesTabix seqnamesTabix,character-method
Manipulate tabix indexed tab-delimited files.	close.TabixFile countTabix headerTabix,TabixFile-method isOpen,TabixFile-method open.TabixFile scanTabix,character,ANY-method scanTabix,character,missing-method scanTabix,TabixFile,GRanges-method scanTabix,TabixFile,IntegerRangesList-method scanTabix,TabixFile,missing-method seqnamesTabix,TabixFile-method TabixFile TabixFile-class TabixFileList TabixFileList-class
Operations on `tabix' (indexed, tab-delimited) files.	scanTabix scanTabix,character,GRanges-method scanTabix,character,IntegerRangesList-method
Quickly test if a BAM file has paired end reads	testPairedEndBam testPairedEndBam,BamFile-method testPairedEndBam,character-method