Updated Tabix bed #729

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merged 21 commits into from Jul 7, 2016

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cmdcolin commented Apr 12, 2016

The PR that @zhjilin contributed for #672 was very useful but it was based off of JBrowse 1.11.6

This updates it to fix conflicts and formatting

The code can parse "BED 6", but doesn't require all 6 columns https://genome.ucsc.edu/FAQ/FAQformat.html#format1 (chr start end name score strand)

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zhjilin Apr 17, 2016

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Thanks and nice work @cmdcolin ! I haven't got time to fix my code, been busy to fix something else.

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zhjilin commented Apr 17, 2016

Thanks and nice work @cmdcolin ! I haven't got time to fix my code, been busy to fix something else.

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cmdcolin Apr 18, 2016

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No problem. I find the tabix BED to be quite useful in a variety of scenarios, so I've used this branch already for a couple of things. For example, it is great with loading junctions.bed files from tophat or with a large list of variants with scores attached. It actually takes forever for flatfile-to-json.pl to load those files containing potentially millions of lines, but is quite fast to convert to tabix

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cmdcolin commented Apr 18, 2016

No problem. I find the tabix BED to be quite useful in a variety of scenarios, so I've used this branch already for a couple of things. For example, it is great with loading junctions.bed files from tophat or with a large list of variants with scores attached. It actually takes forever for flatfile-to-json.pl to load those files containing potentially millions of lines, but is quite fast to convert to tabix

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cmdcolin May 18, 2016

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I think this is done if there is interest in reviewing

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cmdcolin commented May 18, 2016

I think this is done if there is interest in reviewing

@cmdcolin cmdcolin referenced this pull request in elsiklab/gwasviewer May 31, 2016

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BEDTabix class missing #2

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keiranmraine Jun 7, 2016

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I've had a good play with multiple tracks running BED+tabix. Should it be possible to use this with the density plot out the box (Track+load from file, select density) or would that be additional config?

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keiranmraine commented Jun 7, 2016

I've had a good play with multiple tracks running BED+tabix. Should it be possible to use this with the density plot out the box (Track+load from file, select density) or would that be additional config?

@keiranmraine keiranmraine referenced this pull request Jun 7, 2016

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Tabix bed #672

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@keiranmraine it supports the "summary bigwig" when you use the "Track->Open track file or URL" function with the coverage bigwig naming convention (ie. file.bed.gz, file.bed.gz.tbi, file.coverage.bw will become a single track). all the canvasfeatures tracks can use summary bigwigs too via config in trackList.json

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cmdcolin commented Jun 7, 2016

@keiranmraine it supports the "summary bigwig" when you use the "Track->Open track file or URL" function with the coverage bigwig naming convention (ie. file.bed.gz, file.bed.gz.tbi, file.coverage.bw will become a single track). all the canvasfeatures tracks can use summary bigwigs too via config in trackList.json

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cmdcolin Jun 14, 2016

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It might be nice just for completeness sake to allow untabixed BED too. You can already load plain BED with flatfile-to-json.pl but would be good to have the plain JS parser

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cmdcolin commented Jun 14, 2016

It might be nice just for completeness sake to allow untabixed BED too. You can already load plain BED with flatfile-to-json.pl but would be good to have the plain JS parser

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cmdcolin Jul 6, 2016

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I added a plain BED file parser here :)

I also updated this to not include the "matrix header" parsing code as this seemed non-standard. As a workaround to enable flexible header parsing, callbacks called commentCallback and featureCallback can be used to preprocess header directives and features

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cmdcolin commented Jul 6, 2016

I added a plain BED file parser here :)

I also updated this to not include the "matrix header" parsing code as this seemed non-standard. As a workaround to enable flexible header parsing, callbacks called commentCallback and featureCallback can be used to preprocess header directives and features

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There is one other note that I think is important to note about this PR. The files should be named with the particular convention: vcf.gz.tbi or bed.gz.tbi. Having a file like file.bed.gz and file.tbi would not associate the files together

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cmdcolin commented Jul 6, 2016

There is one other note that I think is important to note about this PR. The files should be named with the particular convention: vcf.gz.tbi or bed.gz.tbi. Having a file like file.bed.gz and file.tbi would not associate the files together

cmdcolin added some commits Jul 6, 2016

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I think this is good now, mentioned to @enuggetry about merge! Can go ahead with it?

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cmdcolin commented Jul 7, 2016

I think this is good now, mentioned to @enuggetry about merge! Can go ahead with it?

@enuggetry enuggetry merged commit 8c8d838 into master Jul 7, 2016

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@cmdcolin cmdcolin deleted the tabix_bed branch Jul 10, 2016

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