samView: Call samtools view on a sam/bam file

In sherrillmix/dnar: Miscellaneous functions to deal with bioinformatic analyses

Call samtools view on a sam/bam file

Description

Call samtools view on a sam/bam file

Usage

samView(
  fileName,
  samArgs = "",
  ...,
  samtoolsBinary = "samtools",
  vocal = FALSE,
  samCommand = "view"
)

Arguments

fileName	vector of sam/bam files to read
samArgs	1 element character vector of args to pass to samtools
...	additional arguments for read.sam
samtoolsBinary	location of samtools
vocal	if TRUE print status messages
samCommand	which samtools tool to run

Value

data.frame with columns as read.sam

sherrillmix/dnar documentation built on July 18, 2022, 10:07 p.m.