pslCalcMilliBad: internal function used to determing a psl alignment score.

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

Description

internal function used to determing a psl alignment score.

Usage

  pslCalcMilliBad(psl, isMrna = !pslIsProtein(psl))

Arguments

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

Value

integer. largely undocumented

Author(s)

Mark Cowley, 12 April 2006

Examples

## Note the order within psl differs if import.psl(score=TRUE)
f <- file.path(system.file(package="blat"), "examples", "test.psl")
psl <- import.psl(f, score=FALSE)[1:5,]
pslCalcMilliBad(psl[3,])
psl[3,]

psl <- import.psl(f, score=TRUE)[1:5,]
pslCalcMilliBad(psl[3,])
psl[3,]

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