Rsortbam: Sort bam file and rebuild bai index.

In wzthu/ATACpipe: An Easy-to-use Systematic pipeline for ATACseq data analysis

Sort bam file and rebuild bai index.

Description

Sort bamfile and build index.

Usage

atacBamSort(atacProc, bamInput = NULL, bamOutput = NULL, ...)

## S4 method for signature 'ATACProc'
atacBamSort(atacProc, bamInput = NULL, bamOutput = NULL, ...)

bamsort(bamInput = NULL, bamOutput = NULL, ...)

Arguments

atacProc	ATACProc-class object scalar. It has to be the return value of upstream process: atacSam2Bam.
bamInput	Character scalar. Input bam file path.
bamOutput	Character scalar. Output bam file path.
...	Additional arguments, currently unused.

Value

An invisible ATACProc-class object scalar for downstream analysis.

Author(s)

Wei Zhang

See Also

atacSam2Bam atacBam2Bed

Examples

library(Rsamtools)
ex1_file <- system.file("extdata", "ex1.bam", package="Rsamtools")
bamsort(bamInput = ex1_file)

wzthu/ATACpipe documentation built on Aug. 12, 2022, 7:38 a.m.