getSubSeqsTable: Align and trim sequences for marker/sample pair
In mlgt: Multi-Locus Geno-Typing

Description Usage Arguments Details Value

A list of sequences mapped to both thisMarker and thisSample is created and these sequences are aligned to markerSeq.

  getSubSeqsTable(thisMarker, thisSample, sampleMap,
    fMarkerMap, rMarkerMap, markerSeq, maxVarsToAlign = 30,
    minTotalCount = 500, errorCorrect = FALSE,
    correctThreshold = 0.01, minLength = 70)

`thisMarker`	A specific marker name
`thisSample`	A specific sample name
`sampleMap`	A list of sequence IDs assigned to each marker. Each element named by marker name.
`fMarkerMap`	A list of sequence IDs assigned to each sample using BLAST hits in forward orientation. Each element named by sample name.
`rMarkerMap`	A list of sequence IDs assigned to each sample using BLAST hits in reverse orientation. Each element named by sample name.
`markerSeq`	The sequence of thisMarker
`maxVarsToAlign`	If total assigned sequences exceeds 'minTotalCount', then only the 'maxVarsToAlign' most abundant variants are used.
`minTotalCount`	How many assigned sequences to allow before limiting the number of raw variants to allign.
`errorCorrect`	Use error correection on alignment of raw variants
`correctThreshold`	Maximum proportion of raw reads at which (minor allele) bases and gaps are corrected.
`minLength`	Reads below this length are excluded (they are very likely to be primer-dimers).