Hi @DailyDreaming, this is an interesting approach! However, before diving in can you comment on the following?:

• xsamtools already has built in support for FIFO pipes over gs blobs. It would be preferable to use that here, if possible, unless there’s a reason to prefer this method.
• The main reason to use cloud slicing is to download only the interesting parts of the CRAM file. However, using a stream seems to force the download of the entire file. Or at least all data from the beginning of the file to the portion of interest, which may be a lot. What is the benefit of streaming for this use case?

@xbrianh I'll replace this with the xsamtools method. This will still be used to cover the case where the entire file needs to be streamed in (no or all region args).

This ticket doesn't implement slicing, so by necessity, it's an implementation that forces the download of the whole file. Which is still a valid use case and slicing will only be implemented when a subset of regions is given, otherwise all regions means the entire file. This implementation should be strictly more efficient than the current implementation, since the current implementation downloads/writes the file, then hands it to samtools, which writes another file. Streaming saves the IO for an entire step.