pappewaio / allelicimbalance Goto Github PK

Hi,
I came across your package a couple days ago by searching and found your newly released vignettes. Since I'm working on a project involving calculation of allelic imbalance, thought why not to give it a shot. There was just a confusion for me.
Based on vignettes, one can start with bam files, create an ASEset object and move on. It also says one can start with bcf or vcf files (assuming I already have bcf files created by other tools) but in the same step it needs "reads" object which should be created with AllelicImbalance package from bam files again, that is weird or I didn't get it. The problem is, not all bam files are toy examples and can be huge and the software loads it all into the memory at once, causing crash in R session if computer doesn't have more memory than the file size.
Anyways, starting with bam files or not, it would be nice if you could incorporate a mechanism like in Rsamtools that reads certain number of reads each time not the whole file. For example: BamFileList(bam_files, yieldSize=100000)
Please advice me if I didn't get it right.

Thanks,
Mehdi