1532
89%

Ran 22 Jan 2019 06:05PM UTC

Jobs 1

Files 103

Run time 8min

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Build # 1532

Build Type

push

travis-ci

Committed by

web-flow

Commit Message

Scalable vep annotation in VT (#433)

This PR improves the current annotation pipeline by:
- Add option '--shard_input_files' to shard the input files before annotations.
- Add option '--run_with_garbage_collection' to clean up the VMs in case of failure or cancellation.
- Distribute the annotation workload to VMs more evenly based on the number of variants rather than the number of files.
- Add Integration tests and published a new VEP image.

TODO: update the doc.
Tested: unit tests  & integration tests

Run Details

324 of 324 new or added lines in 11 files covered. (100.0%)

6943 of 7820 relevant lines covered (88.79%)

0.89 hits per line

New Missed Lines in Diff

Lines	Coverage	∆	File
1	0.0	0.0%	gcp_variant_transforms/vcf_to_bq_preprocess.py
4	92.59		gcp_variant_transforms/transforms/write_variants_to_shards.py
5	83.05	1.3%	gcp_variant_transforms/libs/annotation/vep/vep_runner.py
6	68.06	-4.67%	gcp_variant_transforms/pipeline_common.py
11	47.62		gcp_variant_transforms/transforms/annotate_files.py
53	31.15	-4.01%	gcp_variant_transforms/vcf_to_bq.py

Uncovered Existing Lines

Lines	Coverage	∆	File
2	92.41	5.17%	gcp_variant_transforms/libs/annotation/vep/vep_runner_util.py
2	94.93	-1.07%	gcp_variant_transforms/libs/annotation/vep/vep_runner_test.py
7	83.05	1.3%	gcp_variant_transforms/libs/annotation/vep/vep_runner.py

Jobs

ID	Job ID	Ran	Files	Coverage
1	1532.1	22 Jan 2019 06:05PM UTC	103	88.79	Travis Job 1532.1

googlegenomics / gcp-variant-transforms / 1532
89%

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googlegenomics / gcp-variant-transforms / 1532 89%

README BADGES x

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Source Files on build 1532

googlegenomics / gcp-variant-transforms / 1532
89%

README BADGES
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