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Review/add tests for new file formats in HB #127

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sveinugu opened this issue Mar 18, 2020 · 3 comments · May be fixed by #132
Open
3 tasks

Review/add tests for new file formats in HB #127

sveinugu opened this issue Mar 18, 2020 · 3 comments · May be fixed by #132
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@sveinugu
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sveinugu commented Mar 18, 2020

  • BigBed
  • BigWig
  • VCF
@sveinugu
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Including common bounding issues such as empty files

@radmilak
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@sveinugu There is one issue that we never really resolved - it is long ago so I don't remember the exact details, but it has something to do with the possibility of having two bounding region without a space right behind each other. I think in some of the other formats this isn't possible though the new formats are parsed in a different way so the situation is a bit different there.. I think we discussed this and came to the fact that perhaps this is not a problem, also I think implementing this for at least one or several of these new formats was somehow not-trivial, though I can't remember exactly why. I guess we perhaps don't have the time to resolve this now, or what do you think?

@sveinugu sveinugu linked a pull request Jul 7, 2020 that will close this issue
@radmilak
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The tests and also the rest of the file format support is here: https://github.com/hyperbrowser/genomic-hyperbrowser/tree/ft_master/new_fileformats_support. A remaining issue is the bounding regions solution mentioned in my previous comment.

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