Thank you for your useful package cn.mops.
I use your function "getReadCountsFromBAM". However I noticed that starting from Bioconductor version 3.4, the "mode" argument disappeared (I noticed it as I used to count reads from paired-end sequencing data and setting mode="paired").
This change seems to be due to the fact that you started to rely on exomeCopy::countBamInGRanges from Bioc version 3.4 onwards.
It seems in the current Bioc release 3.5 for instance (and in 3.4), paired-end reads are counted twice. Would there be a straightforward way of counting them only once (i.e. to get the same behavior as in Bioc version 3.3 with mode="paired")?
Thanks for your advice.