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Scrub binary files from git history #162
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Sharded BAM reader and a sample read counting pipeline
Its now in the codelabs repository.
--machineType does not have a default of n1-standard-4 in all contexts.
Now that we are doing client-side filtering for strict shard boundaries, we need to ensure that we are requesting the field that the filter will check.
Allow start/end when reading from the API in CountReads, improve script documentation.
Add Genomics API counters for Dataflow UI display.
…tation Implement sample variant annotation dataflow pipeline
Bump utils-java version.
Adding a more comprehensive test for ReadConverter Added gat-tools-java as a dependency to access the Read->SAMRecord converter
Fixing a few bugs in ReadConverter and adding a new test for Sam -> Read -> Sam conversion.
Update to latest version of DataflowSDK.
Also add validation to --output which fixes googlegenomics#31
Bump utils-java.
Implement fallback CoderProvider.
Merge VerifyBamId to master.
Proto2Coder is preferred because it is deterministic.
Switch VerifyBamId to v1 Position objects.
Also default to use gRPC for VariantSimilarity.
Refactor auth.
Also remove obsolete version of JoinNonVariantSegmentsWithVariants.
Refactor options.
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@jirkadanek Thanks so much for these detailed instructions!!! We will make it so. |
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Before: Receiving objects: 100% (6743/6743), 121.52 MiB | 210.00 KiB/s, done.
After: Receiving objects: 100% (6421/6421), 36.37 MiB | 210.00 KiB/s, done.
This change has to be force-pushed. Merging does not do the trick. I am including the exact commands I executed to do this. It might be best if you just run the commands yourself.
Fixes #101
List all files ever in the repository
List all deleted files ever in the repository
Get changelog
Decide what to scrub
Scrub the files from history
Wait for this to complete. It takes a very long time, which proves that scrubbing the files one by one was a bad idea.
Review and push the result
Local clones
Do steps # 8 and # 9 from https://help.github.com/articles/remove-sensitive-data/ on each local clone you have