R/fixSwitches.R

In hsphase: Phasing, Pedigree Reconstruction, Sire Imputation and Recombination Events Identification of Half-sib Families Using SNP Data

# Copyright (C) 2014 Mohammad H. Ferdosi
#
# HSPhase is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.

# HSPhase program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.

# You should have received a copy of the GNU General Public License
# along with this program.  If not, see <http:#www.gnu.org/licenses/>.

fixSW <- function(haplotype,  ohMax = 0, windowsSize = 100, minLength = 100, cpus = 2)
{
	groupMatrix <- groupMatSingle(haplotype, windowsSize, cpus,"haplotype",  ohMax)
	switches <- switchDetector(groupMatrix)
	fixedHaplotype <- addSwitch(haplotype, switches, minLength)
	fixedHaplotype
}