1733
89%

Ran 10 Jun 2019 05:05PM UTC

Jobs 1

Files 109

Run time 8s

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Build # 1733

Build Type

push

travis-ci

Committed by

web-flow

Commit Message

Add support for bgzf. (#484)

Add support for reading of bgzf.
- If the index file is not present, use fusion break to speed up the pipeline.
- Otherwise, parse the index file and read the bgzf in parallel.
- The BGZF can end with .gz or .bgz, and must be in GCS.
- The index file is required to be in the same path as bgzf ending with .tbi.
- Only PyVCF Parser is supported.

Run Details

339 of 339 new or added lines in 10 files covered. (100.0%)

7415 of 8334 relevant lines covered (88.97%)

0.89 hits per line

New Missed Lines in Diff

Lines	Coverage	∆	File
1	97.67	-0.53%	gcp_variant_transforms/beam_io/vcf_header_io.py
2	85.57	-0.38%	gcp_variant_transforms/beam_io/vcf_parser.py
3	74.17	4.06%	gcp_variant_transforms/pipeline_common.py
7	91.88	-4.07%	gcp_variant_transforms/beam_io/vcfio.py
10	35.53	-0.88%	gcp_variant_transforms/vcf_to_bq.py
26	74.26		gcp_variant_transforms/beam_io/bgzf.py

Uncovered Existing Lines

Lines	Coverage	∆	File
1	35.53	-0.88%	gcp_variant_transforms/vcf_to_bq.py

Jobs

ID	Job ID	Ran	Files	Coverage
1	1733.1	10 Jun 2019 05:05PM UTC	109	88.97	Travis Job 1733.1

googlegenomics / gcp-variant-transforms / 1733
89%

README BADGES
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New Missed Lines in Diff

Uncovered Existing Lines

Jobs

Source Files on build 1733

googlegenomics / gcp-variant-transforms / 1733 89%

README BADGES x

Markdown

Textile

RDoc

HTML

Rst

New Missed Lines in Diff

Uncovered Existing Lines

Jobs

Source Files on build 1733

googlegenomics / gcp-variant-transforms / 1733
89%

README BADGES
x