mapInit: Initial mapping.

In gschofl/DR2S: Dual redundant reference sequencing

Description

Short reads (Illumina) and long reads (PacBio or Nanopore) or long reads alone are mapped to a single reference sequence.

Usage

mapInit(x, opts = list(), ...)

Arguments

x	A DR2S object.
opts	List with options passed to the mapper.
...	Additional parameters passed to PileupParam.

Value

A DR2S object.

See Also

Other DR2S mapper functions: cache, clear, createDR2SConf, mapFinal, mapIter, partitionLongreads, polish, refineAlignment, reportCheckedConsensus, report

Examples

## Not run: 
x <- DR2Smap(
  sample = "ID12300527",
  locus = "DPB1*04:01:01:01",
  datadir = "/path/to/data",
  outdir = "/path/to/output"
  ) %>%
  mapInit() %>%
  partitionLongreads() %>%
  mapIter() %>%
  partitionShortreads() %>%
  mapFinal() %>%
  polish() %>%
  report(blockWidth = 60)

## End(Not run)

gschofl/DR2S documentation built on May 17, 2019, 8:40 a.m.