readPsl — readPsl • genecovr

Read psl output

Usage

readPsl(
  filename,
  seqinfo.query = NULL,
  seqinfo.sbjct = NULL,
  metadata = list(),
  ...
)

Arguments

filename: input filename
seqinfo.query: Seqinfo object for query (transcripts)
seqinfo.sbjct: Seqinfo object for subject (reference)
metadata: metadata for AlignmentPairs result
...: additional parameters

Value

AlignmentPairs object

Details

Parse Pattern Space Layout (psl) file; see http://genome.ucsc.edu/FAQ/FAQformat.html for more information on the psl file format

Examples

fn <- system.file("extdata", "transcripts2polished.psl",
      package="genecovr")
ap <- readPsl(fn)
#> reading file /home/runner/work/_temp/Library/genecovr/extdata/transcripts2polished.psl
#> manually inferring seqinfo for query
#> manually inferring seqinfo for subject
#> Processed 239 lines in 0.08 secs