pslScore: calculate the score from a psl alignment

In drmjc/blat: Import/Export functions for UCSC genome BLAT alignments

Description

This calculates the score for a PSL alignment, based on C code from Jim Kent, see comment in pslScore.R. This has been optimised, breaking the problem into smaller chunks.

Usage

  pslScore(psl, isMrna = !pslIsProtein(psl[1, ]))

Arguments

psl	a PSL object
isMrna	logical: protein scores are 3x size of mrna/nucleotide scores.

Value

vector psl alignment score

Author(s)

Mark Cowley, 12 April 2006

Examples

f <- file.path(system.file(package="blat"), "examples", "test.psl")
psl <- import.psl(f, score=FALSE)
psl$score <- pslScore(psl, FALSE)
head(psl)

# or the simpler appraoch
f <- file.path(system.file(package="blat"), "examples", "test.psl")
psl <- import.psl(f, score=TRUE)
head(psl)

drmjc/blat documentation built on May 15, 2019, 2:22 p.m.