mapIter: Iterative mapping.

Description Usage Arguments Value See Also Examples

View source: R/all-generics.R

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

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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(), remapAlignment(), reportCheckedConsensus(), report()

Examples

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## 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() %>%
  report(blockwidth = 60)

## End(Not run)

DKMS-LSL/dr2s documentation built on March 14, 2021, 2:46 p.m.