View source: R/find_spike_contigs.R
x, where !is.null(seqinfo(x))
Find the spike-like contigs in a BAM with both natural and spiked contigs. This started out as glue in some other functions and got refactored out.
something with seqlevels
a DataFrame with spike-in information
The indices have an attribute "mappings", which is a character vector
such that attr(find_spike_contigs(x), "mappings") == standardized
for all contig names in the CRAM/BAM/whatever, and standardized is
the rowname in
spike that corresponds to the original contig name.
indices of which contigs in seqlevels(x) are spike-in contigs
sb <- system.file("extdata", "example.spike.bam", package="spiky", mustWork=TRUE) si <- seqinfo_from_header(sb) data(spike, package="spiky") find_spike_contigs(si, spike=spike)
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