align_contigs: align_contigs

In mskilab/loosends: Classifying loose ends in gGraphs

align_contigs

Description

Align contigs (character vector) to reference Then annotate the segments of the alignment according to reference seqnames

Relies on seqnames –> annotation mapping included as part of the package...

Usage

align_contigs(
  tigs,
  ref,
  primary.only = TRUE,
  remove.decoy = TRUE,
  keep.unaligned = FALSE,
  verbose = FALSE
)

Arguments

tigs	(character)
ref	(RSeqLib::BWA)
primary.only	(logical) default TRUE
keep.unaligned	(logical) keep unaligend contigs?? default FALSE
verbose	(logical) default FALSE
refseq.fn	(character) path to seqnames annotation file (included)

Value

data.table with contig alignment and metadata fields seq, query.seq

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