# Import aligned BAM file format sequences into R / Bioconductor

## Documentation for package ‘Rsamtools’ version 1.4.3

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.
- Package NEWS.

## Help Pages

A B C D F G I N O P R S U misc

Rsamtools-package | 'samtools' aligned sequence utilities interface

## -- A --

asBam | Import, count, index, and other operations on 'BAM' (binary alignment) files.
asBam-method | Import, count, index, and other operations on 'BAM' (binary alignment) files.

## -- B --

bamDirname<- | Views into a set of BAM files
bamExperiment | Views into a set of BAM files
BamFile | Maintain SAM and BAM files
BamFile-class | Maintain SAM and BAM files
bamFlag | Parameters for scanning BAM files
bamFlag<- | Parameters for scanning BAM files
bamIndicies | Views into a set of BAM files
bamPaths | Views into a set of BAM files
bamRanges | Views into a set of BAM files
bamRanges<- | Views into a set of BAM files
bamReverseComplement | Parameters for scanning BAM files
bamReverseComplement<- | Parameters for scanning BAM files
bamSamples | Views into a set of BAM files
bamSamples<- | Views into a set of BAM files
bamSimpleCigar | Parameters for scanning BAM files
bamSimpleCigar<- | Parameters for scanning BAM files
bamTag | Parameters for scanning BAM files
bamTag<- | Parameters for scanning BAM files
BamViews | Views into a set of BAM files
BamViews-class | Views into a set of BAM files
BamViews-method | Views into a set of BAM files
bamWhat | Parameters for scanning BAM files
bamWhat<- | Parameters for scanning BAM files
bamWhich | Parameters for scanning BAM files
bamWhich<- | Parameters for scanning BAM files
BcfFile | Manipulate BCF or VCF files.
BcfFile-class | Manipulate BCF or VCF files.
bcfGeno | Parameters for scanning VCF / BCF files
bcfInfo | Parameters for scanning VCF / BCF files
bcfMode | Manipulate BCF or VCF files.
bcfTrimEmpty | Parameters for scanning VCF / BCF files
bcfWhich | Parameters for scanning VCF / BCF files
bzfile-class | 'samtools' aligned sequence utilities interface

## -- C --

close.BamFile | Maintain SAM and BAM files
close.BcfFile | Manipulate BCF or VCF files.
close.FaFile | Manipulate indexed fasta files.
countBam | Import, count, index, and other operations on 'BAM' (binary alignment) files.
countBam-method | Maintain SAM and BAM files
countBam-method | Views into a set of BAM files
countBam-method | Import, count, index, and other operations on 'BAM' (binary alignment) files.
countFa | Operations on indexed 'fasta' files.
countFa-method | Manipulate indexed fasta files.
countFa-method | Operations on indexed 'fasta' files.

## -- D --

dim-method | Views into a set of BAM files
dimnames-method | Views into a set of BAM files
dimnames<--method | Views into a set of BAM files

## -- F --

FaFile | Manipulate indexed fasta files.
FaFile-class | Manipulate indexed fasta files.
fifo-class | 'samtools' aligned sequence utilities interface
filterBam | Import, count, index, and other operations on 'BAM' (binary alignment) files.
filterBam-method | Maintain SAM and BAM files
filterBam-method | Import, count, index, and other operations on 'BAM' (binary alignment) files.

## -- G --

gzfile-class | 'samtools' aligned sequence utilities interface

## -- I --

index | A base class for managing file references in Rsamtools
indexBam | Import, count, index, and other operations on 'BAM' (binary alignment) files.
indexBam-method | Maintain SAM and BAM files
indexBam-method | Import, count, index, and other operations on 'BAM' (binary alignment) files.
indexFa | Operations on indexed 'fasta' files.
indexFa-method | Manipulate indexed fasta files.
indexFa-method | Operations on indexed 'fasta' files.
isOpen-method | Maintain SAM and BAM files
isOpen-method | Manipulate BCF or VCF files.
isOpen-method | Manipulate indexed fasta files.
isOpen-method | A base class for managing file references in Rsamtools

## -- N --

names-method | Views into a set of BAM files
names<--method | Views into a set of BAM files

## -- O --

open.BamFile | Maintain SAM and BAM files
open.BcfFile | Manipulate BCF or VCF files.
open.FaFile | Manipulate indexed fasta files.

## -- P --

path | A base class for managing file references in Rsamtools
pipe-class | 'samtools' aligned sequence utilities interface

## -- R --

readBamGappedAlignments | GappedAlignments objects
readBamGappedAlignments-method | Maintain SAM and BAM files
readBamGappedAlignments-method | Views into a set of BAM files
readBamGappedAlignments-method | GappedAlignments objects
readPileup | Import samtools 'pileup' files.
readPileup-method | Import samtools 'pileup' files.
Rsamtools | 'samtools' aligned sequence utilities interface
RsamtoolsFile-class | A base class for managing file references in Rsamtools

## -- S --

scanBam | Import, count, index, and other operations on 'BAM' (binary alignment) files.
scanBam-method | Maintain SAM and BAM files
scanBam-method | Views into a set of BAM files
scanBam-method | Import, count, index, and other operations on 'BAM' (binary alignment) files.
scanBamFlag | Parameters for scanning BAM files
scanBamHeader | Import, count, index, and other operations on 'BAM' (binary alignment) files.
scanBamHeader-method | Maintain SAM and BAM files
scanBamHeader-method | Import, count, index, and other operations on 'BAM' (binary alignment) files.
ScanBamParam | Parameters for scanning BAM files
ScanBamParam-class | Parameters for scanning BAM files
ScanBamParam-method | Parameters for scanning BAM files
scanBamWhat | Parameters for scanning BAM files
scanBcf | Operations on 'VCF' or 'BCF' (variant call) files.
scanBcf-method | Manipulate BCF or VCF files.
scanBcf-method | Operations on 'VCF' or 'BCF' (variant call) files.
scanBcfHeader | Operations on 'VCF' or 'BCF' (variant call) files.
scanBcfHeader-method | Manipulate BCF or VCF files.
scanBcfHeader-method | Operations on 'VCF' or 'BCF' (variant call) files.
ScanBcfParam | Parameters for scanning VCF / BCF files
ScanBcfParam-class | Parameters for scanning VCF / BCF files
ScanBcfParam-method | Parameters for scanning VCF / BCF files
scanFa | Operations on indexed 'fasta' files.
scanFa-method | Manipulate indexed fasta files.
scanFa-method | Operations on indexed 'fasta' files.
scanFaIndex | Operations on indexed 'fasta' files.
scanFaIndex-method | Manipulate indexed fasta files.
scanFaIndex-method | Operations on indexed 'fasta' files.
show-method | Views into a set of BAM files
show-method | A base class for managing file references in Rsamtools
show-method | Parameters for scanning BAM files
show-method | Parameters for scanning VCF / BCF files
sortBam | Import, count, index, and other operations on 'BAM' (binary alignment) files.
sortBam-method | Maintain SAM and BAM files
sortBam-method | Import, count, index, and other operations on 'BAM' (binary alignment) files.

## -- U --

unz-class | 'samtools' aligned sequence utilities interface
url-class | 'samtools' aligned sequence utilities interface

## -- misc --

[-method | Views into a set of BAM files