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whatshap / whatshap

Read-based phasing of genomic variants, also called haplotype assembly
https://whatshap.readthedocs.io
MIT License
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Output fewer statistics? #107

Open marcelm opened 8 years ago

marcelm commented 8 years ago

Original report by Tobias Marschall (Bitbucket: tobiasmarschall, GitHub: tobiasmarschall).

While refactoring the code to unify pedigree and single-individual cases in branch genotype-likelihoods, I removed outputting some summary statistics (like the sum of the number of phased blocks). Since WhatsHap now processes all individuals, potentially clustered into families, and all chromosomes, this statistic did not seem overly meaningful.

Since we have whatshap stats now, I think WhatsHap output can in general be a bit more "quiet" and focus on the most important statistics.

Opinions?

marcelm commented 8 years ago

I’d be happy about less output in the default case. In my opinion, it would be sufficient to just print some progress while the program works, perhaps only a single line per chromosome, and then have a few lines of summary statistics at the end, just so that one can see how well the phasing went.