seqinfo_from_header {spiky} | R Documentation

## create seqinfo (and thus a standard chromosome filter) from a BAM/CRAM header

### Description

create seqinfo (and thus a standard chromosome filter) from a BAM/CRAM header

### Usage

    seqinfo_from_header(x, gen = NA, std = FALSE, ret = c("si", "gr"))

### Arguments

`x` | the BAM/CRAM file or its header
`gen` | genome of the BAM/CRAM file, if known (NULL; autodetect)
`std` | standard chromosomes only? (FALSE; will be empty if spikes)
`ret` | return Seqinfo ("si", the default) or GRanges ("gr")? ("si")

### Details

Setting std=TRUE on a spike-in CRAM or BAM will produce an empty result.

### Value

       Seqinfo object or GRanges (or `as(seqinfo, "GRanges")`)

### Examples

      library(Rsamtools)
      fl <- system.file("extdata", "ex1.bam", package="Rsamtools", mustWork=TRUE)

      hdr <- scanBamHeader(BamFile(fl))
      si <- seqinfo_from_header(hdr)
      gr <- seqinfo_from_header(fl, ret="gr")
      stopifnot(identical(gr, as(si, "GRanges")))

      std_si <- seqinfo_from_header(fl, std=TRUE)
      seqlevels(std_si)

      # for comparison with below
      data(spike, package="spiky")
      spike

      # FIXME: add an example with a CRAM instead
      sp <- system.file("extdata", "example.spike.bam", package="spiky")
      sp_gr <- seqinfo_from_header(sp, ret="gr")
      sp_gr

[Package spiky version 1.0.0 Index]