dataflow-java

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Bumps [com.github.samtools:htsjdk](https://github.com/samtools/htsjdk) from 1.128 to 3.0.1. Release notes Sourced from com.github.samtools:htsjdk's releases. 3.0.1 Fix for a long standing vulnerability around temporary directory creation which could expose data to malicious users...

dependabot[bot]

Bumps [junit:junit](https://github.com/junit-team/junit4) from 4.11 to 4.13.1. Release notes Sourced from junit:junit's releases. JUnit 4.13.1 Please refer to the release notes for details. JUnit 4.13 Please refer to the release notes...

dependabot[bot]

Security Policy violation Binary Artifacts

28

_This issue was automatically created by [Allstar](https://github.com/ossf/allstar/)._ **Security Policy Violation** Project is out of compliance with Binary Artifacts policy: binaries present in source code **Rule Description** Binary Artifacts are an...

google-allstar-prod[bot]

There haven't been any updates on this repo in 2 years and the documentation is out-of-date #223 Seems like this repo should be deprecated so as not to confuse customers.

tswast

https://cloud.google.com/genomics/install-genomics-tools doesn't seem to exist.

tswast

In LoadReadsToBigQuery, we currently ignore info filed map in Reads proto. We should export the data in this field to BigQuery too.

nmousavi

nmousavi

deflaux

[WriteBAMTransform](https://github.com/googlegenomics/dataflow-java/blob/master/src/main/java/com/google/cloud/genomics/dataflow/writers/bam/WriteBAMTransform.java) used by [ShardedBAMWriting](https://github.com/googlegenomics/dataflow-java/blob/master/src/main/java/com/google/cloud/genomics/dataflow/pipelines/ShardedBAMWriting.java) assumes that it receives reads in order. Add a group by and a sort operation so that input reads can be read from multiple BAM shards...

deflaux

Identity By State variant streamer fails with write error

1

I am trying to apply the IdentityByState pipeline to my variant data, but it reliably (n=4) fails with a write error. Error message: ``` (dd6b6f2b6ea510df): Workflow failed. Causes: (dd6b6f2b6ea5110a): S07:VariantStreamer/ParDo(RetrieveVariants)+VariantStreamer/ParDo(ConvergeVariantsList)+JoinNonVariantSegmentsWithVariants.BinShuffleAndCombineTransform/ParDo(BinVariants)+JoinNonVariantSegmentsWithVariants.BinShuffleAndCombineTransform/GroupByKey/Reify+JoinNonVariantSegmentsWithVariants.BinShuffleAndCombineTransform/GroupByKey/Write...

pbilling