cigarToBlock: Convert cigar and starts to qStarts, tStarts, blockSizes as...
In sherrillmix/dnar: Miscellaneous functions to deal with bioinformatic analyses

cigarToBlock

R Documentation

Convert cigar and starts to qStarts, tStarts, blockSizes as in blat

Description

Convert cigar and starts to qStarts, tStarts, blockSizes as in blat

Usage

cigarToBlock(cigars, starts, startEnds = FALSE)

Arguments

`cigars`	vector of SAM cigar strings
`starts`	vector of starting positions in target
`startEnds`	if FALSE single line with comma separated starts, if TRUE data.frame with single start, end and id column

Value

dataframe with qStarts,tStarts,sizes if !startEnds or dataframe with starts, ends and ids if startEnds

Examples

cigars<-c('100M','10H10M1000H','10M10I20M10D2M','10S10M10H','100M10000N100M')
starts<-1:5
cigarToBlock(cigars,starts)
cigarToBlock(cigars,starts,startEnds=TRUE)

sherrillmix/dnar documentation built on July 18, 2022, 10:07 p.m.