read.psl: Read PSL file(s) outputted by BLAT
In hiReadsProcessor: Functions to process LM-PCR reads from 454/Illumina data

Description Usage Arguments Value Note See Also Examples

Given filename(s), the function reads the PSL file format from BLAT as a data frame and performs basic score filtering if indicated. Any other file format will yield errors or erroneous results. Make sure there is no header row! See required columns in pslCols.

1 2	read.psl(pslFile = NULL, bestScoring = TRUE, asGRanges = FALSE, removeFile = TRUE, parallel = FALSE)

`pslFile`	PSL filename, or vector of filenames, or a pattern of files to import.
`bestScoring`	report only best scoring hits instead of all hits. Default is TRUE. Score is calculated by matches-misMatches-qBaseInsert-tBaseInsert.
`asGRanges`	return a GRanges object instead of a dataframe. Default is FALSE
`removeFile`	remove the PSL file(s) after importing. Default is 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`.

a dataframe reflecting psl file type. If asGRanges=TRUE, then a GRanges object.

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, startgfServer, blatSeqs, read.blast8, read.BAMasPSL, pslToRangedObject, write.psl

## Not run: 
data(psl)
pslFile <- tempfile()
write.psl(psl, filename = pslFile)
head(read.psl(pslFile = pslFile))
# read many PSL files matching the regex #
psl <- read.psl(pslFile = "processed.*.psl$")

## End(Not run)