mapFinal: Final mapping (long reads and short reads).

In gschofl/DR2S: Dual redundant reference sequencing

Description

Partitioned long reads and partitioned or unpartitioned short reads are mapped against the consensus sequences inferred at mapIter. Indels are included in pileup.

Usage

mapFinal(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, mapInit, 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.