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Rsamtools (version 1.22.0)

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

Description

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

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Version

Version

1.22.0

License

Artistic-2.0 | file LICENSE

Maintainer

Bioconductor Package Maintainer

Last Published

February 15th, 2017

Functions in Rsamtools (1.22.0)

applyPileups

Apply a user-provided function to calculate pile-up statistics across multiple BAM files.
Deprecated and Defunct

Rsamtools Deprecated and Defunct
FaFile

Manipulate indexed fasta files.
deprecated

Deprecated functions
BcfFile

Manipulate BCF files.
indexTabix

Compress and index tabix-compatible files.
ApplyPileupsParam

Parameters for creating pileups from BAM files
headerTabix

Retrieve sequence names defined in a tabix file.
BamViews

Views into a set of BAM files
BamFile

Maintain and use BAM files
quickBamFlagSummary

Group the records of a BAM file based on their flag bits and count the number of records in each group
ScanBamParam

Parameters for scanning BAM files
Rsamtools-package

'samtools' aligned sequence utilities interface
pileup

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

Operations on `BCF' files.
RsamtoolsFileList

A base class for managing lists of Rsamtools file references
RsamtoolsFile

A base class for managing file references in Rsamtools
BamInput

Import, count, index, filter, sort, and merge `BAM' (binary alignment) files.
TabixFile

Manipulate tabix indexed tab-delimited files.
readPileup

Import samtools 'pileup' files.
testPairedEndBam

Quickly test if a BAM file has paired end reads
Compression

File compression for tabix (bgzip) and fasta (razip) files.
FaInput

Operations on indexed 'fasta' files.
TabixInput

Operations on `tabix' (indexed, tab-delimited) files.
seqnamesTabix

Retrieve sequence names defined in a tabix file.
PileupFiles

Represent BAM files for pileup summaries.
ScanBcfParam-class

Parameters for scanning BCF files