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standalone flip fails when "reduced.chrom.sizes" provided, should go lexicographical #91

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sergpolly opened this issue Jan 25, 2021 · 1 comment

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@sergpolly
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e.g. , when pairtools flip --chroms-path hg38.reduced.chrom.sizes p1.pairs, where hg38.reduced.chrom.sizes does not have un-assembled contigs - it fails when encounters unrecognized name - e.g. KeyError: 'chrUn_KI270438v1'

in the same situation pairtools parse behaves differently - it flips what it can according to hg38.reduced.chrom.sizes and flips lexicographically everything else

no big deal - but we'd rather have it documented - to fix later

@sergpolly sergpolly changed the title standalone flip fails when "reduced.chrom.sizes" provided, should do lexicographical sort standalone flip fails when "reduced.chrom.sizes" provided, should go lexicographical Jan 25, 2021
@agalitsyna agalitsyna mentioned this issue Apr 6, 2022
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@agalitsyna
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Thanks, resolved by: #117
@sergpolly , it would be great if you can check this toy example with unannotated chromosome: https://github.com/open2c/pairtools/blob/7480fb500a3d4db2c43ea9d98f4c65764c68a1e5/tests/data/mock.4flip.pairs

If that's what you expect, then let's close it!

@open2c open2c locked and limited conversation to collaborators Apr 20, 2022
@agalitsyna agalitsyna converted this issue into discussion #130 Apr 20, 2022

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