Code "improvement" suggestions

[nurfatimaj]

Hello!

Can I suggest the following changes to the code?

1. Should this line https://github.com/35ajstern/palm/blob/31ad155df23c667a45cd78f1d8ef06fd9d480e96/lik.py#L87
   be changed to locusDerTimes,locusAncTimes = parse_clues(args.times+'.timeb')? I have created a pull request Changed input file extension from .palm to .timeb #6 for this.
2. When I tried to test for selection in the last 8 epochs, I received a "division by zero" error when estimating likelihood in one of the SNPs. I managed to get around it by adding/subtracting bit in following lines:
   https://github.com/35ajstern/palm/blob/31ad155df23c667a45cd78f1d8ef06fd9d480e96/palm_utils/deterministic_utils.py#L89
   https://github.com/35ajstern/palm/blob/31ad155df23c667a45cd78f1d8ef06fd9d480e96/palm_utils/deterministic_utils.py#L92
   https://github.com/35ajstern/palm/blob/31ad155df23c667a45cd78f1d8ef06fd9d480e96/palm_utils/deterministic_utils.py#L118
   https://github.com/35ajstern/palm/blob/31ad155df23c667a45cd78f1d8ef06fd9d480e96/palm_utils/deterministic_utils.py#L121
   But I am not sure how legit this fix is? Could you please have a look?

Thanks a lot!

[standard-aaron]

Hi! Busy week for me but

(1) I will implement (i thought I fixed this before...sorry!)

and (2) i don't think this is a valid fix, as bit (iirc) is an important variable that determines allele polarization.

Can you send me a minimal reproducible example? (ajstern at-sign berkeley dot edu)