quickBamFlagSummary {Rsamtools} | R Documentation

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

### Description

`quickBamFlagSummary` groups the records of a BAM file based on their flag bits and counts the number of records in each group.

### Usage

    quickBamFlagSummary(file, ..., param=ScanBamParam(), main.groups.only=FALSE)

    ## S4 method for signature 'character'
    quickBamFlagSummary(file, index=file, ..., param=ScanBamParam(),
        main.groups.only=FALSE)

    ## S4 method for signature 'list'
    quickBamFlagSummary(file, ..., param=ScanBamParam(), main.groups.only=FALSE)

### Arguments

`file, index` | For the character method, the path to the BAM file to read, and to the index file of the BAM file to read, respectively. For the list() method, `file` is a named list with elements “qname” and “flag” with content as from `scanBam`.
`...` | Additional arguments, perhaps used by methods.
`param` | An instance of `ScanBamParam`. This determines which records are considered in the counting.
`main.groups.only` | If `TRUE`, then the counting is performed for the main groups only.

### Value

Nothing is returned. A summary of the counts is printed to the console unless redirected by `sink`.

### Author(s)

H. Pages

### References

http://samtools.sourceforge.net/

### See Also

`scanBam`, `ScanBamParam`.

`BamFile` for a method for that class.

### Examples

    bamfile <- system.file("extdata", "ex1.bam", package="Rsamtools",
                           mustWork=TRUE)
    quickBamFlagSummary(bamfile)

[Package Rsamtools version 2.0.3 Index]