Hi,

I am experiencing an issue with ATACseqQC 1.27.1 after updating from 1.18.

Code below worked in 1.18 but in 1.27.1 gives the following error:

Error in strsplit(SE, split = ".", fixed = TRUE) : non-character argument

seqinformation <- seqinfo(TxDb.genome3.own) #custom TxDb from a genome and gtf annotation (same with BSgenome)
bamf <- "nodup_paired_test.bam"
seqlev <- "Scaffold2"
which <- as(seqinformation[seqlev], "GRanges")
bamal <- readBamFile(bamf, which = which, asMates=TRUE, bigFile=TRUE)
bamsal <- shiftGAlignmentsList(bamal)

This is in addition to the RAM usage for shiftGAlignmentsList() issue I have commented on jfmay's question.

ATACseqQC shiftGAlignmentsList() problem

Best,

Dani