createKnownAlleleList: Create variantMap object from allele alignment
Description
Create a variantMap object to store known
alleles for a marker
Usage
createKnownAlleleList(markerName, markerSeq, alignedAlleleFile, alignFormat = "msf", sourceName = alignedAlleleFile, userAlignment = FALSE)
Arguments
markerName
A specific marker name
alignedAlleleFile
a sequence alignment
alignFormat
the format of alignedAlleleFile. "msf"
(the default) or "fasta"
sourceName
A character string to record the source
of the alignment. Defaults to the value of
alignedAlleleFile
userAlignment
The specified 'alignedAlleleFile'
already includes the marker sequence. Default = FALSE.
Details
To compare variants produced using mlgt the
sequences of the known alleles must be aligned to the
same marker used to find the variants. The resulting
sub-sequence alignment may have identical sequences for
different alleles. If that happens, those alleles are
condensed into one and their names concatenated. User can
supply files with marker sequences pre-aligned to the
reference alleles.