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Add tribble codec (read support) for GENCODE files to htsjdk #3277

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droazen opened this issue Jul 17, 2017 · 2 comments
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Add tribble codec (read support) for GENCODE files to htsjdk #3277

droazen opened this issue Jul 17, 2017 · 2 comments
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@jonn-smith
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Engine Funcotator HTSJDK
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Engine-4.0

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@droazen
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droazen commented Jul 17, 2017

We'll need to support both hg38 and hg19 inputs.
@droazen droazen mentioned this issue Jul 17, 2017
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@droazen droazen added this to the Engine-4.0 milestone Jul 17, 2017
@jonn-smith
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@lbergelson suggested looking at the IGV Tribble codec for Gencode:
https://github.com/igvteam/igv/blob/8b4fa74fc51d20f91c467f123f6e8b8bf23698e5/src/org/broad/igv/feature/tribble/GFFCodec.java

I'll start by checking this out.

@lbergelson
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It looks like there's an hg37 lift over of the hg38 data that uses the same format so that should suffice hopefully.

jonn-smith added a commit that referenced this issue Jul 24, 2017
@jonn-smith
Adding in codec to read from Gencode GTF files. Fixes #3277
f3e9e09
jonn-smith added a commit that referenced this issue Aug 4, 2017
@jonn-smith
Adding in codec to read from Gencode GTF files. Fixes #3277
960338c 
Includes tests for both hg19 and hg38.
jonn-smith added a commit that referenced this issue Aug 11, 2017
@jonn-smith
Adding in codec to read from Gencode GTF files. Fixes #3277
b12a3ef 
Includes tests for both hg19 and hg38.
jonn-smith added a commit that referenced this issue Aug 28, 2017
@jonn-smith
Adding in codec to read from Gencode GTF files. Fixes #3277
82dd2ab 
Includes tests for both hg19 and hg38.
jonn-smith added a commit that referenced this issue Sep 12, 2017
@jonn-smith
Adding in codec to read from Gencode GTF files. Fixes #3277
e63d482 
Includes tests for both hg19 and hg38.
jonn-smith added a commit that referenced this issue Oct 30, 2017
@jonn-smith
Adding in codec to read from Gencode GTF files. Fixes #3277
3df331a 
Includes tests for both hg19 and hg38.
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