Deduper review!

[maddygriz]

Looks good just a couple suggestions.

1. Can you sort by RNAME and position? Then the original positions will come in a logical order all on the same chromosome.

2. With your adjust_position function, you say "only adjust if the first letter isn't an M" but what if there is an indel in the middle of the read?

3. I think you are thinking of the CIGAR string backward. You keep the position the same with the Ms. The examples in the adjust position should be 50 and 60. The first one will be the same since there is no soft clipping at the beginning and the second one will add 5 because of the soft clipping. If this doesn't make sense I can try and explain it either over slack or in person next week.

4. The ID technique is cool but I think it might be better implemented as a dictionary and the ID is the key. This will be faster than searching through a set.

5. Your functions look like good standalone pieces of code, but I have a feeling you will need a few more like get_UMI out of the header specifically.