Package: Rsamtools 2.23.1

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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NEWS

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

Peer review:

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-2.23.0(bioc 3.21)Rsamtools-2.22.0(bioc 3.20)

dataimportsequencingcoveragealignmentqualitycontrolbioconductor-packagecore-packagecurlbzip2xz-utilszlibcpp

15.48 score 27 stars 572 packages 3.2k scripts 48k downloads 138 mentions 138 exports 31 dependencies

Last updated 14 hours agofrom:21a5945271. Checks:OK: 1 WARNING: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 27 2024
R-4.5-win-x86_64WARNINGNov 27 2024
R-4.5-linux-x86_64WARNINGNov 27 2024
R-4.4-win-x86_64WARNINGNov 27 2024
R-4.4-mac-x86_64WARNINGNov 27 2024
R-4.4-mac-aarch64WARNINGNov 27 2024
R-4.3-win-x86_64WARNINGNov 27 2024
R-4.3-mac-x86_64WARNINGNov 27 2024
R-4.3-mac-aarch64WARNINGNov 27 2024

Exports:applyPileupsApplyPileupsParamasBamasBcfasMatesasMates<-asSambamDirname<-bamExperimentBamFileBamFileListbamFlagbamFlag<-bamFlagANDbamFlagAsBitMatrixbamFlagTestbamIndiciesbamMapqFilterbamMapqFilter<-bamPathsbamRangesbamRanges<-bamReverseComplementbamReverseComplement<-BamSamplerbamSamplesbamSamples<-bamSimpleCigarbamSimpleCigar<-bamTagbamTag<-bamTagFilterbamTagFilter<-BamViewsbamWhatbamWhat<-bamWhichbamWhich<-BcfFileBcfFileListbcfFixedbcfGenobcfInfobcfModebcfSamplesbcfTrimEmptybcfWhichbgzipbgzipTabixclose.BamFileclose.BcfFileclose.FaFileclose.RsamtoolsFileListclose.TabixFilecountBamcountFacountTabixFaFileFaFileListfilterBamFLAG_BITNAMESgetSeqgzindexgzindex<-headerTabixidxstatsBamindexindex<-indexBamindexBcfindexFaindexTabixisIncompleteisOpenmergeBamobeyQnameobeyQname<-open.BamFileopen.BcfFileopen.FaFileopen.RsamtoolsFileListopen.TabixFilephred2ASCIIOffsetpileupPileupFilesPileupParamplpFilesplpFlagplpFlag<-plpMaxDepthplpMaxDepth<-plpMinBaseQualityplpMinBaseQuality<-plpMinDepthplpMinDepth<-plpMinMapQualityplpMinMapQuality<-plpParamplpWhatplpWhat<-plpWhichplpWhich<-plpYieldAllplpYieldAll<-plpYieldByplpYieldBy<-plpYieldSizeplpYieldSize<-qnamePrefixEndqnamePrefixEnd<-qnameSuffixStartqnameSuffixStart<-quickBamCountsquickBamFlagSummaryquickCountBamrazipreadPileupscanBamscanBamFlagscanBamHeaderScanBamParamscanBamWhatscanBcfscanBcfHeaderScanBcfParamscanFascanFaIndexscanTabixseqinfoseqnamesTabixshowsortBamTabixFileTabixFileListtestPairedEndBamyieldSizeyieldSize<-yieldTabix

Dependencies:askpassBHBiocGenericsBiocParallelBiostringsbitopscodetoolscpp11crayoncurlformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangeshttrIRangesjsonlitelambda.rmimeopensslR6RhtslibS4VectorssnowsysUCSC.utilsXVectorzlibbioc

An Introduction to Rsamtools

Martin Morgan, Samuel Busayo

Rendered fromRsamtools-Overview.Rmdusingknitr::rmarkdownon Nov 27 2024.

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

Readme and manuals

Help Manual

Help pageTopics
'samtools' aligned sequence utilities interfaceRsamtools-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 filesApplyPileupsParam 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 filesasMates 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 filesbamDirname<- 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 functionsBamSampler 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 groupquickBamFlagSummary 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 Rsamtoolsindex 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 referencesclose.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 filesbamFlag 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 filesbcfFixed 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 readstestPairedEndBam testPairedEndBam,BamFile-method testPairedEndBam,character-method