bam.read: bam.read

In mskilab/skidb: Collection of R functions for accessing and parsing flat file dumps of common databases and external software used by @mskilab.

bam.read

Description

Loads entire bam or slice into data.table or dumps to csv via samtools call (instead of Rsamtools like read.bam)

Usage

bam.read(
  bam,
  out.file = NULL,
  region = NULL,
  fields = c("seq"),
  tags = c("MD", "BX"),
  nlines = NULL,
  estimate.lines = TRUE,
  skip = NULL,
  chunksize = 1e+05,
  mc.cores = 1,
  min.mapq = 0,
  samtools.flag = "",
  verbose = TRUE
)

Arguments

bam	bam file
out.file	file to dump csv to, if null returns data.table
tags	which tags to extract from bam file
nlines	number of lines in bam file if known, otherwise will be estimated
estimate.lines	flag whether to count lines or just estimate using bam.size if nlines is not provided (default = TRUE)
skip	how many lines to skip
mc.cores	how many threads to use for parsing
min.mapq	integer min mapping quality
samtools.flag	additoinal samtools flag to use
verbose	flag

Author(s)

Marcin Imielinski

mskilab/skidb documentation built on Feb. 6, 2023, 2:49 a.m.