What I'm trying to achieve is as follows:
- read a bam file into R
- perform a series of filtering and edit some tags
- write the object out into a new bam file
What I realized was that tracking tags are really hard. When I read in the alignments, I'm hoping to also read in all the tags, so that I can modify them and create a new bam file. I have not seen any functions that can do that. The scan functions in Rsamtools seems to require a prior knowledge of the tags and only keeps track of the tags specified. I would highly appreciate it if you could point me to the correct package/function.
Thanks in advance