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open2c / pairtools

Extract 3D contacts (.pairs) from sequencing alignments
MIT License
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semantic confusion in stats #64

Open sergpolly opened 6 years ago

sergpolly commented 6 years ago

We used to have following fields in the stats before https://github.com/mirnylab/pairsamtools/commit/85ddfb309591cb0b8bea56130ca5648afeac77d6

total_unmapped
total_single_sided_mapped
dedup/n_unmapped

Now after https://github.com/mirnylab/pairsamtools/commit/85ddfb309591cb0b8bea56130ca5648afeac77d6 we are collecting stats in the dedup step the same way, as before is parse, so this specialized field

dedup/n_unmapped

is gone now.

What's confusing, to me at least, is to have a field total_unmapped in stats and have there - "unmapped on both sides" ...

Should we rename it to: total_both_sides_unmapped as suggested by @golobor , or something like that. Or should we make total_unmapped to include both total_both_sides_unmapped and total_single_sided_mapped ? @nvictus ?

sergpolly commented 6 years ago

here's what we need to implement:

screen shot 2018-01-22 at 3 45 01 pm
agalitsyna commented 2 years ago

@sergpolly Is it still relevant? Seems like we are okay with current version, which is an input to multiqc. Changing the pairs standards will need to modify multiqc as well.