findAndRemoveVector: Find and trim vector sequence from reads.
In hiReadsProcessor: Functions to process LM-PCR reads from 454/Illumina data

Description Usage Arguments Value Note See Also

This function facilitates finding and trimming of long/short fragments of vector present in LM-PCR products. The algorithm looks for vector sequence present anywhere within the read and trims according longest contiguous match on either end of the read. Alignment is doing using BLAT

1 2	findAndRemoveVector(reads, Vector, minLength = 10, returnCoords = FALSE, parallel = TRUE)

`reads`	DNAStringSet object containing sequences to be trimmed for vector.
`Vector`	DNAString object containing vector sequence to be searched in reads.
`minLength`	integer value dictating minimum length of trimmed sequences to return. Default is 10.
`returnCoords`	return the coordinates of vector start-stop for the matching reads. Defaults to FALSE.
`parallel`	use parallel backend to perform calculation with `BiocParallel`. Defaults to TRUE. If no parallel backend is registered, then a serial version is ran using `SerialParam`.

DNAStringSet object with Vector sequence removed from the reads. If returnCoords=TRUE, then a list of two named elements "hits" & "reads". The first element, "hits" is a GRanges object with properties of matched region and whether it was considered valid denoted by 'good.row'. The second element, "reads" is a DNAStringSet object with Vector sequence removed from the reads.

If parallel=TRUE, then be sure to have a parallel backend registered before running the function. One can use any of the following MulticoreParam SnowParam

pairwiseAlignSeqs, vpairwiseAlignSeqs, pslToRangedObject, blatSeqs, read.blast8, findAndTrimSeq