Aidan Lakshman

Just a quick update since it's been a week on this--I did get the data from @gevro, and I am able to reproduce the bug in a docker container. I...

It's tough to know what the problem is without the code that caused the error--what was the input that caused this message?

Finally getting around to this--I'm working on adding an optional parameter to display extended ASCII values for BStrings. It would be ideal for to maintain the "1 position = 1...

Example implementation is available at https://github.com/ahl27/Biostrings/commit/494d81af7e087f6c59a7bfa0a2f05243a4199973 ~~Cons of this approach are that it only supports ASCII values from 0:254. There's a limitation of the internal value not supporting embedded 0s...

To Hervé's comment--That's a good point...I'll take a longer look at it tomorrow. Maybe there's a cleaner solution than this first pass. Maybe it would be easier to just build...

@gevro thats an interesting use-case...I'm unfortunately not sure if it's possible without a significant overhaul of the entire `XVector` class, which is somewhat beyond the scope of Biostrings. The `BString`...

Just some more further thoughts, since I've been thinking about this for a while now... For completeness sake, I should also mention that there is an argument to be made...

> I'm analyzing kinetic PacBio data, from the tags 'ip' and 'pw' in PacBio BAM files. These are encoded as 'B,C' type tags: https://pacbiofileformats.readthedocs.io/en/13.0/BAM.html . Per SAM specifications, 'B,C' type...

Sorry for the slow reply--I've been thinking about this more over this week and looking into the codebase. First, a temporary workaround: ```r subset_arbitrary_values_by_cigar reference mapping ops_to_remove

No worries! Since I've been thinking about it, try just using this solution based on the `doubleBString` prototype that should scale much better and have your desired input format: ```r...