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projectglow
An open-source toolkit for large-scale genomic analysis
## What changes are proposed in this pull request? 1. Temporarily stop Hail tests (until these are upgraded for where breaking Hail changes are presently failing) 2. Fix broken links...
Signed-off-by: William Brandler ## What changes are proposed in this pull request? Adding in the GATK to the glow docker container was having some issues building the glow docker container...
Vulnerable shared library might make glow-spark3 vulnerable. Can you help upgrade to patch versions?
Hi, @karenfeng , @henrydavidge , I'd like to report a vulnerable dependency in **io.projectglow:glow-spark3_2.12:1.1.2**. ### Issue Description I noticed that **io.projectglow:glow-spark3_2.12:1.1.2** directly depends on **org.apache.spark:spark-core_2.12:3.1.2** in the [pom](https://repo1.maven.org/maven2/io/projectglow/glow-spark3_2.12/1.1.2/glow-spark3_2.12-1.1.2.pom). However, as...
Hi, is it possible that the split and normalize transformers are significantly slower than `bcftools norm`? We just tried splitting a large 190GB VCF file with 800 samples from https://dataportal.answerals.org/home...
Pulling the latest tagged release of glow (v 1.2.1), the docker files don't seem to be updated. Below shows the variables as in `build.sh` file in `docker/databricks/` ``` DOCKER_HUB="projectglow" DATABRICKS_RUNTIME_VERSION="9.1"...
I just tried glow with PySpark 3.2.0: ```python spark.read.parquet(OUTPUT_PATH) ``` ```java Py4JJavaError: An error occurred while calling o62.parquet. : java.lang.NoSuchMethodError: org.apache.spark.sql.catalyst.plans.logical.LogicalPlan.transformAllExpressions(Lscala/PartialFunction;)Lorg/apache/spark/sql/catalyst/plans/logical/LogicalPlan; at io.projectglow.sql.optimizer.ReplaceExpressionsRule$.apply(hlsOptimizerRules.scala:33) at io.projectglow.sql.optimizer.ReplaceExpressionsRule$.apply(hlsOptimizerRules.scala:31) at org.apache.spark.sql.catalyst.rules.RuleExecutor.$anonfun$execute$2(RuleExecutor.scala:211) at scala.collection.LinearSeqOptimized.foldLeft(LinearSeqOptimized.scala:126) at...
Hi, My setup is Spark v3.1.3 with Hadoop v3.2.2 and PySpark v3.1.2 and latest glow.py. I'm trying to read some BGEN files into GLOW from my a jupyter notebook. I...
I am running an example notebook from Databricks. I have installed glow version 1.1.1 for this cluster. I am encountering an error with `glow.register(spark)`. What am I missing? ``` import...
Converting a Hail matrix table to glow works fine, but when you try to write out or perform downstream glow functions on the data it fails, ``` import hail as...
I've been testing logistic regression with `correction="approx-firth"`. I noticed that during the preliminary calculation of score-logistic p-values (ie, the non-firth-corrected p-values that are used to determine whether further refinement is...
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An open-source toolkit for large-scale genomic analysis