feat: Sampling without replacement option for simgenotype #194
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aryarm
reviewed
Feb 20, 2023
aryarm
reviewed
Feb 20, 2023
| @@ -113,6 +122,9 @@ def output_vcf( | |||
| for ind, sample in enumerate(vcf.samples): | |||
| sample_dict[sample] = ind | |||
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| # initialize hap_used array which should contain list of lists for each reference sample's genome and what segment has been used for each | |||
| haps_used = [[] for samp in range(len(vcf.samples)*2)] | |||
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does this scale well for large numbers of samples? I recall that python dynamically allocates memory for list items, even within list comprehensions
so it might have to repeatedly make copes whilst constructing this list?
Honestly, it might not even matter in terms of time, compared to other things in our code. I just wanted to confirm
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Thanks for adapting all this to not rely on Pandas! Overall this seems great. The primary concern is with regard to how random the haplotypes will be. Also, in admix-simu, we ensured that the haplotype changes at each segment breakpoint. It seems like this code may not do that? Look forward to this being added to haptools!
Update haplotype choices for replacement so it doesn't switch when it isn't changing segments
Ensured that every segment we grab is randomly selecting a sample and not just the first sample in the list over and over again
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Added sampling without replacement flag in simgenotype
--no_replacementthat allows the user to run simgenotype and when outputting the newly simulated variants, the reference vcf used will be sampled without replacement per region.Code adapted from Amy Williams PR that originally used pandas but now uses numpy and lists