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

## Documentation for package ‘Rsamtools’ version 2.29.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

A B C D F G H I L M N O P Q R S T U Y misc

Rsamtools-package | 'samtools' aligned sequence utilities interface

## -- A --

applyPileups | Apply a user-provided function to calculate pile-up statistics across multiple BAM files.
applyPileups-method | Represent BAM files for pileup summaries.
ApplyPileupsParam | Parameters for creating pileups from BAM files
ApplyPileupsParam-class | Parameters for creating pileups from BAM files
asBam | Import, count, index, filter, sort, and merge 'BAM' (binary alignment) files.
asBam-method | Import, count, index, filter, sort, and merge 'BAM' (binary alignment) files.
asBcf | Operations on 'BCF' files.
asBcf-method | Operations on 'BCF' files.
asMates | Maintain and use BAM files
asMates-method | Maintain and use BAM files
asMates<- | Maintain and use BAM files
asMates<--method | Maintain and use BAM files
asSam | Import, count, index, filter, sort, and merge 'BAM' (binary alignment) files.
asSam-method | Import, count, index, filter, sort, and merge 'BAM' (binary alignment) files.

## -- B --

bamDirname<- | Views into a set of BAM files
bamExperiment | Views into a set of BAM files
BamFile | Maintain and use BAM files
BamFile-class | Maintain and use BAM files
BamFileList | Maintain and use BAM files
BamFileList-class | Maintain and use BAM files
bamFlag | Parameters for scanning BAM files
bamFlag<- | Parameters for scanning BAM files
bamFlagAND | Parameters for scanning BAM files
bamFlagAsBitMatrix | Parameters for scanning BAM files
bamFlagTest | Parameters for scanning BAM files
bamIndicies | Views into a set of BAM files
bamMapqFilter | Parameters for scanning BAM files
bamMapqFilter<- | Parameters for scanning 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
BamSampler | Deprecated functions
BamSampler-class | Deprecated functions
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
bamTagFilter | Parameters for scanning BAM files
bamTagFilter<- | 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
bamWhich<--method | Parameters for scanning BAM files
BcfFile | Manipulate BCF files.
BcfFile-class | Manipulate BCF files.
BcfFileList | Manipulate BCF files.
BcfFileList-class | Manipulate BCF files.
bcfFixed | Parameters for scanning BCF files
bcfGeno | Parameters for scanning BCF files
bcfInfo | Parameters for scanning BCF files
bcfMode | Manipulate BCF files.
bcfSamples | Parameters for scanning BCF files
bcfTrimEmpty | Parameters for scanning BCF files
bcfWhich | Parameters for scanning BCF files
bgzip | 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.
bzfile-class | 'samtools' aligned sequence utilities interface

## -- C --

close.BamFile | Maintain and use BAM files
close.BcfFile | Manipulate BCF files.
close.FaFile | Manipulate indexed fasta files.
close.RsamtoolsFileList | A base class for managing lists of Rsamtools file references
close.TabixFile | Manipulate tabix indexed tab-delimited files.
countBam | Import, count, index, filter, sort, and merge 'BAM' (binary alignment) files.
countBam-method | Maintain and use BAM files
countBam-method | Views into a set of BAM files
countBam-method | Import, count, index, filter, sort, and merge 'BAM' (binary alignment) files.
countFa | Operations on indexed 'fasta' files.
countFa-method | Manipulate indexed fasta files.
countFa-method | Operations on indexed 'fasta' files.
countTabix | Manipulate tabix indexed tab-delimited files.
cycle_bins | Use filters and output formats to calculate pile-up statistics for a BAM file.

## -- 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
distinguish_nucleotides | Use filters and output formats to calculate pile-up statistics for a BAM file.
distinguish_strands | Use filters and output formats to calculate pile-up statistics for a BAM file.

## -- F --

FaFile | Manipulate indexed fasta files.
FaFile-class | Manipulate indexed fasta files.
FaFileList | Manipulate indexed fasta files.
FaFileList-class | Manipulate indexed fasta files.
fifo-class | 'samtools' aligned sequence utilities interface
filterBam | Import, count, index, filter, sort, and merge 'BAM' (binary alignment) files.
filterBam-method | Maintain and use BAM files
filterBam-method | Import, count, index, filter, sort, and merge 'BAM' (binary alignment) files.
FLAG_BITNAMES | Parameters for scanning BAM files

## -- G --

getSeq-method | Manipulate indexed fasta files.
gzfile-class | 'samtools' aligned sequence utilities interface
gzindex | Manipulate indexed fasta files.
gzindex-method | Manipulate indexed fasta files.
gzindex<- | Manipulate indexed fasta files.
gzindex<--method | Manipulate indexed fasta files.

## -- H --

hasUnmappedMate | Parameters for scanning BAM files
headerTabix | Retrieve sequence names defined in a tabix file.
headerTabix-method | Manipulate tabix indexed tab-delimited files.
headerTabix-method | Retrieve sequence names defined in a tabix file.

## -- I --

idxstatsBam | Import, count, index, filter, sort, and merge 'BAM' (binary alignment) files.
idxstatsBam-method | Maintain and use BAM files
idxstatsBam-method | Import, count, index, filter, sort, and merge 'BAM' (binary alignment) files.
ignore_query_Ns | Use filters and output formats to calculate pile-up statistics for a BAM file.
include_deletions | Use filters and output formats to calculate pile-up statistics for a BAM file.
include_insertions | Use filters and output formats to calculate pile-up statistics for a BAM file.
index | A base class for managing file references in Rsamtools
index-method | A base class for managing file references in Rsamtools
index-method | A base class for managing lists of Rsamtools file references
index<- | A base class for managing file references in Rsamtools
index<--method | A base class for managing file references in Rsamtools
index<--method | A base class for managing lists of Rsamtools file references
indexBam | Import, count, index, filter, sort, and merge 'BAM' (binary alignment) files.
indexBam-method | Maintain and use BAM files
indexBam-method | Import, count, index, filter, sort, and merge 'BAM' (binary alignment) files.
indexBcf | Operations on 'BCF' files.
indexBcf-method | Manipulate BCF files.
indexBcf-method | Operations on 'BCF' files.
indexFa | Operations on indexed 'fasta' files.
indexFa-method | Manipulate indexed fasta files.
indexFa-method | Operations on indexed 'fasta' files.
indexTabix | Compress and index tabix-compatible files.
isDuplicate | Parameters for scanning BAM files
isFirstMateRead | Parameters for scanning BAM files
isIncomplete-method | Maintain and use BAM files
isMateMinusStrand | Parameters for scanning BAM files
isMinusStrand | Parameters for scanning BAM files
isNotPassingQualityControls | Parameters for scanning BAM files
isNotPrimaryRead | Parameters for scanning BAM files
isOpen-method | Maintain and use BAM files
isOpen-method | Manipulate BCF files.
isOpen-method | Manipulate indexed fasta files.
isOpen-method | Represent BAM files for pileup summaries.
isOpen-method | A base class for managing file references in Rsamtools
isOpen-method | A base class for managing lists of Rsamtools file references
isOpen-method | Manipulate tabix indexed tab-delimited files.
isPaired | Parameters for scanning BAM files
isProperPair | Parameters for scanning BAM files
isSecondaryAlignment | Parameters for scanning BAM files
isSecondMateRead | Parameters for scanning BAM files
isUnmappedQuery | Parameters for scanning BAM files

## -- L --

left_bins | Use filters and output formats to calculate pile-up statistics for a BAM file.

## -- M --

max_depth | Use filters and output formats to calculate pile-up statistics for a BAM file.
mergeBam | Import, count, index, filter, sort, and merge 'BAM' (binary alignment) files.
mergeBam-method | Maintain and use BAM files
mergeBam-method | Import, count, index, filter, sort, and merge 'BAM' (binary alignment) files.
min_base_quality | Use filters and output formats to calculate pile-up statistics for a BAM file.
min_mapq | Use filters and output formats to calculate pile-up statistics for a BAM file.
min_minor_allele_depth | Use filters and output formats to calculate pile-up statistics for a BAM file.
min_nucleotide_depth | Use filters and output formats to calculate pile-up statistics for a BAM file.

## -- N --

names-method | Views into a set of BAM files
names-method | A base class for managing lists of Rsamtools file references
names<--method | Views into a set of BAM files

## -- O --

obeyQname | Maintain and use BAM files
obeyQname-method | Maintain and use BAM files
obeyQname<- | Maintain and use BAM files
obeyQname<--method | Maintain and use BAM files
open.BamFile | Maintain and use BAM files
open.BcfFile | Manipulate BCF files.
open.FaFile | Manipulate indexed fasta files.
open.RsamtoolsFileList | A base class for managing lists of Rsamtools file references
open.TabixFile | Manipulate tabix indexed tab-delimited files.

## -- P --

path | A base class for managing file references in Rsamtools
path-method | A base class for managing file references in Rsamtools
path-method | A base class for managing lists of Rsamtools file references
phred2ASCIIOffset | Use filters and output formats to calculate pile-up statistics for a BAM file.
pileup | Use filters and output formats to calculate pile-up statistics for a BAM file.
pileup-method | Use filters and output formats to calculate pile-up statistics for a BAM file.
PileupFiles | Represent BAM files for pileup summaries.
PileupFiles-class | Represent BAM files for pileup summaries.
PileupFiles-method | Represent BAM files for pileup summaries.
PileupParam | Use filters and output formats to calculate pile-up statistics for a BAM file.
PileupParam-class | Use filters and output formats to calculate pile-up statistics for a BAM file.
pipe-class | 'samtools' aligned sequence utilities interface
plpFiles | Represent BAM files for pileup summaries.
plpFlag | Parameters for creating pileups from BAM files
plpFlag<- | Parameters for creating pileups from BAM files
plpMaxDepth | Parameters for creating pileups from BAM files
plpMaxDepth<- | Parameters for creating pileups from BAM files
plpMinBaseQuality | Parameters for creating pileups from BAM files
plpMinBaseQuality<- | Parameters for creating pileups from BAM files
plpMinDepth | Parameters for creating pileups from BAM files
plpMinDepth<- | Parameters for creating pileups from BAM files
plpMinMapQuality | Parameters for creating pileups from BAM files
plpMinMapQuality<- | Parameters for creating pileups from BAM files
plpParam | Represent BAM files for pileup summaries.
plpWhat | Parameters for creating pileups from BAM files
plpWhat<- | Parameters for creating pileups from BAM files
plpWhich | Parameters for creating pileups from BAM files
plpWhich<- | Parameters for creating pileups from BAM files
plpYieldAll | Parameters for creating pileups from BAM files
plpYieldAll<- | Parameters for creating pileups from BAM files
plpYieldBy | Parameters for creating pileups from BAM files
plpYieldBy<- | Parameters for creating pileups from BAM files
plpYieldSize | Parameters for creating pileups from BAM files
plpYieldSize<- | Parameters for creating pileups from BAM files

## -- Q --

qnamePrefixEnd | Maintain and use BAM files
qnamePrefixEnd-method | Maintain and use BAM files
qnamePrefixEnd<- | Maintain and use BAM files
qnamePrefixEnd<--method | Maintain and use BAM files
qnameSuffixStart | Maintain and use BAM files
qnameSuffixStart-method | Maintain and use BAM files
qnameSuffixStart<- | Maintain and use BAM files
qnameSuffixStart<--method | Maintain and use BAM files
query_bins | Use filters and output formats to calculate pile-up statistics for a BAM file.
quickBamFlagSummary | Group the records of a BAM file based on their flag bits and count the number of records in each group
quickBamFlagSummary-method | Maintain and use BAM files
quickBamFlagSummary-method | Group the records of a BAM file based on their flag bits and count the number of records in each group

## -- R --

razip | 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.
readPileup | Import samtools 'pileup' files.
readPileup-method | Import samtools 'pileup' files.
Rsamtools | 'samtools' aligned sequence utilities interface
RsamtoolsFile | A base class for managing file references in Rsamtools
RsamtoolsFile-class | A base class for managing file references in Rsamtools
RsamtoolsFileList | A base class for managing lists of Rsamtools file references
RsamtoolsFileList-class | A base class for managing lists of Rsamtools file references

## -- S --

scanBam | Import, count, index, filter, sort, and merge 'BAM' (binary alignment) files.
scanBam-method | Maintain and use BAM files
scanBam-method | Views into a set of BAM files
scanBam-method | Deprecated functions
scanBam-method | Import, count, index, filter, sort, and merge 'BAM' (binary alignment) files.
scanBamFlag | Parameters for scanning BAM files
scanBamHeader | Import, count, index, filter, sort, and merge 'BAM' (binary alignment) files.
scanBamHeader-method | Maintain and use BAM files
scanBamHeader-method | Import, count, index, filter, sort, and merge '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 'BCF' files.
scanBcf-method | Manipulate BCF files.
scanBcf-method | Operations on 'BCF' files.
scanBcfHeader | Operations on 'BCF' files.
scanBcfHeader-method | Manipulate BCF files.
scanBcfHeader-method | Operations on 'BCF' files.
ScanBcfParam | Parameters for scanning BCF files
ScanBcfParam-class | Parameters for scanning BCF files
ScanBcfParam-method | Parameters for scanning BCF files
ScanBVcfParam-class | Parameters for scanning 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.
scanTabix | Operations on 'tabix' (indexed, tab-delimited) files.
scanTabix-method | Manipulate tabix indexed tab-delimited files.
scanTabix-method | Operations on 'tabix' (indexed, tab-delimited) files.
seqinfo-method | Maintain and use BAM files
seqinfo-method | Manipulate indexed fasta files.
seqnamesTabix | Retrieve sequence names defined in a tabix file.
seqnamesTabix-method | Manipulate tabix indexed tab-delimited files.
seqnamesTabix-method | Retrieve sequence names defined in a tabix file.
show-method | Parameters for creating pileups from BAM files
show-method | Maintain and use BAM files
show-method | Views into a set of BAM files
show-method | Manipulate indexed fasta files.
show-method | Represent BAM files for pileup summaries.
show-method | A base class for managing file references in Rsamtools
show-method | Parameters for scanning BAM files
show-method | Parameters for scanning BCF files
show-method | Deprecated functions
show-method | Use filters and output formats to calculate pile-up statistics for a BAM file.
sortBam | Import, count, index, filter, sort, and merge 'BAM' (binary alignment) files.
sortBam-method | Maintain and use BAM files
sortBam-method | Import, count, index, filter, sort, and merge 'BAM' (binary alignment) files.

## -- T --

TabixFile | Manipulate tabix indexed tab-delimited files.
TabixFile-class | Manipulate tabix indexed tab-delimited files.
TabixFileList | Manipulate tabix indexed tab-delimited files.
TabixFileList-class | Manipulate tabix indexed tab-delimited files.
testPairedEndBam | Quickly test if a BAM file has paired end reads
testPairedEndBam-method | Quickly test if a BAM file has paired end reads

## -- U --

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

## -- Y --

yieldSize | A base class for managing file references in Rsamtools
yieldSize-method | A base class for managing file references in Rsamtools
yieldSize-method | A base class for managing lists of Rsamtools file references
yieldSize<- | A base class for managing file references in Rsamtools
yieldSize<--method | A base class for managing file references in Rsamtools
yieldSize<--method | A base class for managing lists of Rsamtools file references
yieldTabix | Deprecated functions
yieldTabix-method | Deprecated functions

## -- misc --

[-method | Views into a set of BAM files