search

JetBrains-Research / jbr

JBR Genome Browser
https://doi.org/10.1093/bioinformatics/btab376
11 stars 0 forks source link

Specialized ArithmeticTrackView for BedGraph files and the like #45

Open dievsky opened 7 years ago

dievsky commented 7 years ago

Right now, the ArithmeticTrackView provides binned data. It doesn't make much sense for sparse BedGraph-type files with identical structure, like the ones we use for miRNA expression data. Arguably, it also doesn't make much sense for fixed step files.

It would be nice if there were a special ArithmeticTrackView for such cases, which would preserve the common structure of each file. At this moment, however, the structure of a BW file is well-hidden behind the summarization abstraction, which makes it difficult to extract. So this is an idea for the future, at best.

iromeo commented 7 years ago

Not clear what to do if user tries to load two BedGraph files with different structure

dievsky commented 7 years ago

@iromeo Fail with an exception, naturally. This specialized track view would be used only for files with matching structure.

dievsky commented 7 years ago

@iromeo as far as I understand, a40de5447da439823f945cb1fc4bbb8d196016ec solves this?

iromeo commented 7 years ago

@dievsky Yes, more or less. We don't do it automatically, just let user selected checkbox if he is sure about underlying tracks format details. Better to do it automatically, but not clear how to do it better.

We cannot check all input files format before showing dialog, it may take some noticeable time, e.g. if file are from NFS. So maybe we can show user default dialog suggesting binnned track, and before processing we can compare files structure and chose processing algorithm automatically.

Let's leave this issue opened, I'll try to implement this "auto" mode.

dievsky commented 5 years ago

It would seem there are currently no plans to implement this feature. We should probably close the issue.