Ben Weisburd

not clear how to profile django app

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##### Description I have a django app, but am not sure how to get vprof graphs for the `python manage.py runserver` dev. server. ##### How to reproduce ##### Actual results...

java.lang.ArrayIndexOutOfBoundsException when creating tabix index

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## Bug Report ### Affected tool(s) or class(es) gatk SortVcf ### Affected version(s) Mac OS X 10.16 x86_64; OpenJDK 64-Bit Server VM 1.8.0_322-b06; Deflater: Intel; Inflater: Intel; Provider GCS is...

TribbleIndexedFeatureReader throws "TribbleException: there aren't enough columns .." on large files unless there's a tabix index

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### Verify This is the same Issue as https://github.com/broadinstitute/gatk/issues/4761 I got the error below when running picard liftover on the bravo-dbsnp-all.vcf.gz (GRCh38 => GRCh37). I'm reposting this because, even though...

readiness probes don't run

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I've defined a readiness probe that's supposed to run a shell script as documented in https://kubernetes.io/docs/tasks/configure-pod-container/configure-liveness-readiness-probes#define-readiness-probes It works when deployed to GKE, but on kube-solo the pod never transitions to...

How can you set cluster username / password, or pass --insecure-bind-address to kube-apiserver ?

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I'm trying to deploy the cockpit container (https://github.com/cockpit-project/cockpit) to a kube-solo cluster, but can't figure out how to use cockpit's authentication mechanism with kube-solo. When I deploy to google container...

Allow histogram.py and other scripts to be imported/used as python modules

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Hi, I'd like to generate histograms to standard out in my python script, and currently have to do `os.system("echo '%s' | historgram.py" % "\n".join(values))` It would be great if I...

When mates mismap to the same remote region of the genome, group them into intervals that can be fetched in a single I/O operation to improve I/O speed.

Include additional fields in the json output

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Since the json files are easier to parse, it would be nice to include all info from the vcf in the json output, including the filter field and sample genome...

This is the error I get when trying to build on MacOS: ``` wm103-772:~/bin/Nirvana $ dotnet --version 5.0.205 wm103-772:~/bin $ git clone https://github.com/Illumina/Nirvana.git Cloning into 'Nirvana'... remote: Enumerating objects: 21499,...

Test code to create expanded tables for genotype fields.

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Hi guys, here's the code I was using to test query runtimes with expanded-out genotype tables. Still needs code: - to add family-based indexes (pending figuring out sample ids) based...