computegphmm: Compute GPHMM log probability.

In gphmm: Generalized Pair Hidden Markov Chain Model for Sequence Alignment

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

computegphmm('TAGC', 'AAG')
computegphmm('TAGC', 'AAG', qv = 30)

gphmm documentation built on Oct. 2, 2017, 5:03 p.m.