Error in coverage: seqnames required #3
Description
Hello,
Thank you for your nice package.
I have been using megadepth for some time and I have never had a problem. Nevertheless, today I tried to compute the coverage of a bigwig file in a bed region and it gave me the following error.
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'as.data.frame': seqnames required
Since this error was given by a custom function internally using megadepth::get_coverage(), I decided to try the example given in the megadepth vignette.
Here is my code:
library(megadepth)
example_bw <- system.file("tests", "test.bam.all.bw",
package = "megadepth", mustWork = TRUE
)
annotation_file <- system.file("tests", "testbw2.bed",
package = "megadepth", mustWork = TRUE
)
get_coverage(
example_bw,
op = "mean",
annotation = annotation_file
)
And here is the error:
unsorted interval: chr10 4359156 4359188
, falling back to slower matching (doesn't affect BAM processing)
For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth.
building whole annotation region map done
2 chromosomes for annotated regions read
1 chromosomes for annotated regions read, collapsed
total number of annotations in collapsed: 1
Processing /home/amitjavila/R/x86_64-pc-linux-gnu-library/4.2/megadepth/tests/test.bam.all.bw
Error in asMethod(object) : seqnames required
I don't know what can be happening.
If you can help me solve this, it would be great.
Thank you very much.