mapIter: Iterative mapping.

In gschofl/DR2S: Dual redundant reference sequencing

Description

Partitioned long reads are mapped against the MSA consensus sequence of each haplotype. Indels are excluded from pileup. New reference consensus sequences for both alleles are inferred.

Usage

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

Arguments

x	A DR2S object.
opts	Named 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, mapInit, 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.