gphmm (version 0.99.0)

computegphmm: Compute GPHMM log probability.

Description

computegphmm returns GPHMM log probability for a read and a reference sequence.

Usage

computegphmm(read, ref, parameters = initializeGphmm(), qv = 20,
  output = "long")

Arguments

read

- chr str.

ref

- chr str.

parameters

- list of GPHMM parameters, can be created by initializeGphmm().

qv

- float, quality value, default is 20.

output

- if 'long', output is a list with path, read, ref and log GPHMM proba, else output is just the log GPHMM proba.

Examples

# NOT RUN {
computegphmm('TAGC', 'AAG')
computegphmm('TAGC', 'AAG', qv = 30)
# }