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tl/dr: mask missing samples under the hood for step 1 and step 2 of GloWGR for quantitative and binary traits. Currently this is only done for step 2 of binary...

williambrandler

Failed fit in approx firth throws ValueError that is never caught. This situation should be handled more gracefully and the correctionSucceeded flag probably should be set to False. https://github.com/projectglow/glow/blob/master/python/glow/gwas/approx_firth.py#L166

bcajes

Integrating glow into pipeline

1

Hi, I'm fairly new to pyspark and glow. Is a way to start the spark and glow session in a python script instead of the python shell or jupyter notebook?...

linchihfan

Option to consider last allele as reference in BGEN reader

1

Our BGEN reader always considers the first allele to be the reference. However, the [BGEN spec](https://www.well.ox.ac.uk/~gav/bgen_format/spec/latest.html) does not codify the position of the ref allele, and it can vary from...

henrydavidge

kianfar77

reading VCF as a streaming datasource in python

2

When I read VCFs as a stream in scala, it works. But the same code in python doesn't start the stream or display anything. Thoughts? Scala: ![Screen Shot 2021-04-01 at...

williambrandler

Improve pipe transformer observability

1

We have a situation where possibly the pipe transformer, running VEP, is throwing data specific errors. We have no visibility into what if any errors VEP is reporting (mostly because...

dmoore247

Cannot flatten info field names containing points

2

Hi, I just tried to load a VCF file where info fields' names contained points: ``` ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO=...

Hoeze

The `mean_substitute` function works on real data, but the minimal example in the API fails, ``` df = spark.createDataFrame([Row(unsubstituted_values=[0, 1, 2, 3, -1, None])]) df.select(glow.mean_substitute('unsubstituted_values').alias('substituted_values')).collect() ``` `AnalysisException: Invalid call to...

williambrandler

Add tips to troubleshooting page

1

Users often accidentally make the following mistakes, which we should address in the [troubleshooting](https://glow.readthedocs.io/en/latest/troubleshooting.html) page: - Installing `glow` with Pypi, rather than `glow.py` - In v1.0.0: failing to set the...

karenfeng