loosereads_wrapper: loosereads_wrapper

In mskilab/loosends: Classifying loose ends in gGraphs

loosereads_wrapper

Description

wrapper for obtaining reads + mates around loose ends and realigning

Usage

loosereads_wrapper(
  ranges = GRanges(),
  tbam = "/dev/null",
  nbam = "/dev/null",
  ref = "/dev/null",
  bowtie = FALSE,
  bowtie.ref = "/dev/null",
  bowtie.dir = "/dev/null",
  id = "",
  outdir = "./",
  pad = 5000,
  mask = "/dev/null",
  cleanup = TRUE,
  verbose = FALSE
)

Arguments

ranges	(GRanges) loose end GRanges
tbam	(character) path to normal bam
nbam	(character) optional, path to normal bam
ref	(character) path to reference .fasta
bowtie	(logical) use bowtie for realignment?
bowtie.ref	(character) basename of bowtie references
bowtie.dir	(character) dirname of bowtie
id	(character) sample name
outdir	(character)
pad	(numeric)
mask	(character) path to GRanges mask
cleanup	(logical) remove temporary files? default TRUE
verbose	(logical)

Value

data.table of reads + mates

mskilab/loosends documentation built on Aug. 24, 2023, 8:08 a.m.