Read a genomic alignment in PAF format

Source: R/IO.r

See the package vignette for detailed information on the file format and its representation as an R object.

read_paf(file_name, tibble = FALSE, include_tags = TRUE)

Arguments

file_name

Path to the .paf file
tibble

logical If TRUE, the genomic alignments are returned as a tidy tbl_df
include_tags

logical if TRUE (default) read additional information about each alignment encoded as PAF tags. Setting this to FALSE will speed up parsing of paf alignments, specially those with large CIGAR strings/

Value

Either a pafr object, which acts as a data.frame, or a tbl_df containing information on genomic alignments. The contents of this table are described in detail in the pafr package vingette.

Examples

ali <- read_paf( system.file("extdata", "fungi.paf", package="pafr") )
ali

#> pafr object with 2501 alignments (36.5Mb)
#>  8 query seqs
#>  8 target seqs
#>  11 tags: NM, ms, AS, nn, tp, cm, s1, s2, dv, cg, zd