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addSequence not in JVM #5306

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konradjk opened this issue Feb 11, 2019 · 3 comments

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commented Feb 11, 2019

Easy-peasy to reproduce:

rg = hl.get_reference('GRCh38')
rg.add_sequence('gs://hail-common/references/Homo_sapiens_assembly38.fasta.gz',
                'gs://hail-common/references/Homo_sapiens_assembly38.fasta.fai')

throws:

Py4JError: is.hail.variant.ReferenceGenome.addSequence does not exist in the JVM
@tpoterba

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commented Feb 11, 2019

this is before initialization?

@konradjk

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commented Feb 11, 2019

like hl.init? no, after

@tpoterba

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commented Feb 11, 2019

ah, it's just totally broken.

tpoterba added a commit to tpoterba/hail that referenced this issue Feb 11, 2019

danking added a commit that referenced this issue Feb 14, 2019

Fix add_sequence (#5308)
* Fix add_sequence

fixes #5306

* Add test

* Fix

* liftover uses scala object

tpoterba added a commit to tpoterba/hail that referenced this issue Feb 15, 2019

Fix add_sequence (hail-is#5308)
* Fix add_sequence

fixes hail-is#5306

* Add test

* Fix

* liftover uses scala object
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