R: bamReader: Connection to BAM file for reading access.

bamReader {rbamtools} | R Documentation

## bamReader: Connection to BAM file for reading access.

### Description

The bamReader function constructs and returns an S4 object of class bamReader. The bamReader object represents a connection to an opened BAM-file. When an indexname is given or idx=TRUE, the function tries to load an existing BAM-index.

### Usage

    bamReader(filename,indexname,idx=FALSE,verbose=0)

### Arguments

`filename` | Filename of BAM-file to be opened for reading.

`indexname` | Optional: Name of BAM-index file

`idx` | Logical

`verbose` | Numeric: Quantifies the extent of textual feedback (levels: 0,1,2).

### Author(s)

Wolfgang Kaisers

### Examples

    bam<-system.file("extdata","accepted_hits.bam",package="rbamtools")
    reader<-bamReader(bam)
    #
    align<-getNextAlign(reader)
    name(align)
    position(align)
    bamClose(reader)
    #
    # Open reader and initialize BAM-index
    reader<-bamReader(bam,idx=TRUE)
    indexInitialized(reader)

[Package rbamtools version 2.16.17 Index]