processPrimers: Processes a dataset with Primer IDs

In HIVDiversity/MotifBinner2: Processes NGS Primer ID Datasets

Description

Applies a series of operations to the input dataset that generates consensus sequences from raw (or preprocessed) datasets containing Primer IDs.

Usage

processPrimers(fwd_reads_file = NULL, rev_reads_file = NULL,
  output_dir = NULL, prefix_for_names = NULL,
  operation_list = c("loadData"), intermediate_reports = TRUE,
  verbosity = 0, report_type = c("html", "pdf"), ...)

Arguments

fwd_reads_file	The name of the fastq file with the forward reads.
rev_reads_file	The name of the fastq file with the reverse reads.
output_dir	The directory in which the output must be produced.
prefix_for_names	The basename to use for naming output.
operation_list	The list of operations to apply to the input data.
intermediate_reports	Should intermediate reports be produced after each operations? (Useful for debugging)
verbosity	The output level. 0 = no output. 1 = info about which operation is currently running. 2 = info about progress of current operation. 3 = super verbose debugging output.
report_type	vector of types of reports to procude. Valid options: 'html', 'pdf'.

HIVDiversity/MotifBinner2 documentation built on May 6, 2019, 6:44 p.m.