report: Report the final haplotype sequences.

In gschofl/DR2S: Dual redundant reference sequencing

Description

Report the final haplotype sequences.

Usage

report(x, whichMap, ...)

Arguments

x	A DR2S object.
whichMap	Which mapping do we want to report. Will choose mapFinal or mapIter in this order as available.
...	Additional arguments passed to methods.

Details

report will create a report directory containing the consensus sequences map{1,2,3}.{A,B}.{readtype}.{mapper}.unchecked.fa, an html alignment file map{1,2,3}.aln.{readtype}.{mapper}.unchecked.html, a pairwise alignment file map{1,2,3}.{A,B}.{readtype}.{mapper}.unchecked.pair, and a tab-separated file problems.{readtype}.{mapper}.tsv reporting positions with potentially problematic results.

To finalise the consensus sequences open the pairwise alignment file and save it replacing unchecked with checked in the file name. In the checked file manual edits can be performed. After the pairwise alignment is verified call reportCheckedConsensus.

Value

Side effect

See Also

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

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.