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Feature density for in-memory adaptor #913

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hkmoon opened this Issue Jul 28, 2017 · 3 comments

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@hkmoon
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hkmoon commented Jul 28, 2017

Currently, I am using GTF, GFF in-memory adaptor which is really useful and very straightforward.
However, when I zoom-out, it does not give any histogram of the feature density.
Can I make histogram by changing some configuration? Or, is there no feature density transition for in-memory adaptor cases?

@cmdcolin

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cmdcolin commented Jul 31, 2017

There is code for histograms to be generated dynamically from feature data but I think what's missing for the in-memory is that it doesn't implement the stats calculations like getGlobalStats. Therefore the genome browser doesn't get any clues as to when to display the histograms. That's just a guess though

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cmdcolin commented Jul 31, 2017

The particular function that is missing from the in-memory store classes is actually called getRegionFeatureDensities.

Note that you can do a workaround which is that you can pre-generate a "bigwig coverage" file (bedtools genomecov helps with this), but maybe that isn't as helpful as an auto calculated feature density

@hkmoon

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hkmoon commented Aug 1, 2017

Thank you for the clarifying it. I thought it was due to the my configuration.
I suppose that the getRegionFeatureDensities function is a quite heavy operation especially on the big files unless the index files are provided.

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