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.
We have changed the read-counting procedure due to errors that were reported by several users in the last Bioc release. For simplicity, we have used the read-counting function of "exomecn.mops" which worked well empirically. However, for some purposes (such as whole genome sequencing with medium or low coverage) the original function might work better. I currently do not find time to re-implement this function (with paired-end reads only counted once at the middle position), but if you -- or any other user -- would implement it (or update the function of the former cn.mops versions), I would be happy to include it in the package! I am sorry that I cannot give a more positive reply!
Thanks for your explanations.
Could you please provide a pointer to the errors that were reported with the previous "getReadCountsFromBAM" function?
It would help me to understand if the counting I did using cn.mops in Bioc 3.3 gave accurate results, as well as maybe provide some ideas on how to reimplement/update that function (as per your suggestion).