ksw2_gg_align: Global alignment of 2 strings

In Ahhgust/MMDIT: Mitochondrial mixture project

Description

This performs global pairwise alignment between a pair of sequences. It returns the number of cigar operations and the operations (M, I, D, optionally =/X if extended CIGARs are used) (ops vector) and the operation positions (opPos vector)

Usage

ksw2_gg_align(
  Tseq,
  Qseq,
  opPos,
  ops,
  sc_mch = 1L,
  sc_mis = -2L,
  gapo = 2L,
  gape = 1L,
  extended = TRUE
)

Arguments

Tseq	(a string from the DNA alphabet)
Qseq	(like Tseq, but different)
opPos	(integer vector that is modified. It is the position of the cigar operation)
ops	(these are the cigar operations themselves. there encoded as their integer representations, e.g., int('M')
sc_mch	(the score for a match)
sc_mis	(the penalty for a mismatch)
gapo	(gap open penalty)
gape	(gap extend penalty)
extended	(changes M [Match or Mismatch] to =/X [Match or Mismatch, respectively] in the CIGAR)

Details

Written by Heng Li with small tweaks by August Woerner

Ahhgust/MMDIT documentation built on Jan. 27, 2021, 11:48 a.m.