build_contigs_wrapper: build_contigs_wrapper

In mskilab/loosends: Classifying loose ends in gGraphs

build_contigs_wrapper

Description

build_contigs_wrapper

Usage

build_contigs_wrapper(
  gr,
  reads.dt,
  ref,
  window = 5000,
  assembly.region = 1000,
  stride = 500,
  pseudo.contigs = TRUE,
  low.mappability.gr = GRanges(),
  unassembled.gr = GRanges(),
  verbose = FALSE
)

Arguments

gr	(GRanges) which breakpoint do we care about
reads.dt	(data.table)
ref	(BWA object)
window	(numeric) how many bases around window to consider for assembly (default 5e3)
assembly.region	(numeric) how many bases at a time to consider for assembly (default 1e3)
stride	(numeric) stride for tiling window (default 500)
pseudo.contigs	(logical) include pseudo-contigs from discordant read clustering? default TRUE
low.mappability.gr	(GRanges) path to GRanges containing low mappability bases
unassembled.gr	(GRanges) path to GRanges containing unassembled regions
verbose	(logical) default FALSE

Value

data.table with contig alignments

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