[BioC] summarizeOverlaps - circular MT

[Stefanie Tauber]

Dear list,

when I try to count human reads vs a human transcript database, I get the
following error:


library(GenomicFeatures)
library(biomaRt)

Here I construct my human transcript database:

ensembl = useDataset("hsapiens_gene_ensembl",mart=useMart("ensembl"))

res = getBM(attributes = "ensembl_transcript_id", filters =
("biotype","status"),values=list("protein_coding","known"),mart = ensembl)

humanDb = makeTranscriptDbFromBiomart(biomart = "ensembl", dataset =
"hsapiens_gene_ensembl",transcript_ids = as.character(res[,1]))
 
tx = transcriptsBy(humanDb) 


The reads are an GappedAlignments object:
reads

GappedAlignments with 11791172 alignments and 0 elementMetadata cols:
                    seqnames strand       cigar    qwidth     start       end
                       <Rle>  <Rle> <character> <integer> <integer> <integer>
        SRR015293.3        3      *         32M        32 186338939 186338970
        SRR015293.5       16      *         32M        32  72094409  72094440
        SRR015293.7        1      *         32M        32 159683461 159683492
        SRR015293.9        4      *         32M        32 155529684 155529715
       SRR015293.10        4      *         32M        32 110632783 110632814


This is working fine:
counts = assays(summarizeOverlaps(tx, reads, mode = "Union"))$counts

Method "IntersectionStrict" does not work:
 counts1 = assays(summarizeOverlaps(tx, liver, mode = "IntersectionStrict"))$counts
Error in assays(summarizeOverlaps(tx, liver, mode = "IntersectionStrict")) : 
  error in evaluating the argument 'x' in selecting a method for function
'assays': Error in queryHits(findOverlaps(query, subject, maxgap = maxgap,
minoverlap = minoverlap,  : 
  error in evaluating the argument 'x' in selecting a method for function
'queryHits': Error in .findOverlaps.circle(circle.length, seqselect(queryRanges,
qIdxs),  : 
  overlap type "within" is not yet supported for circular sequence MT


What can I do? Do I have to omit all genes on the MT?

Best,
Stefanie