suggested API about bamread HOT 4 OPEN

I agree with all, but I'll leave 2) as an exercise for someone else since it is a lot of work for what is likely to be a surprisingly small gain in speed (try it yourself with read_full vs read_sparse to see).

I already support using flags. See here: https://github.com/pyranges/bamread/blob/master/bamread/src/bamread.pyx#L17

from bamread.

I should also support writing bams, but I use bams ever so seldom that I've never gotten around to it (and I am not completely sure how to do it either).

from bamread.

The current functions contain some extra stuff to make sure the data is valid for pyranges like

if start < 0 or end < 0: continue

I guess I should create new similar ones to use for the standalone library so that it acts completely like pysam.

from bamread.

(Just writing notes to self here)

I guess we can alias read_bam to read_sam in __init__.py since I do not think pysam cares about the distinction.

read_sam = read_bam

Worst case we need to change this to not be binary I think: samfile = pysam.AlignmentFile(filename, "rb")

from bamread.