448
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Ran 13 Mar 2018 08:42PM UTC

Jobs 1

Files 47

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Build # 448

Build Type

push

travis-ci

Committed by

web-flow

Commit Message

Add integration tests for some options #106 (#130)

Add integration test for the following options:

- reference_names: tested on valid-4.2.vcf. Used "20 Y" as the reference_names.
- split_alternate_allele_info_fields: set this field to false and validate there is a column AF in BQ.
- allow_malformed_records: created a new file "invalid-4.0-POS-empty" based on "valid-4.0.vcf" by removing the POS value for the first entry.
- representative_header_file: created a new file "invalid-4.0-AF-field-removed.vcf" by removing "AF" field from "valid-4.0.vcf".
- merge_option_none: created a new folder containing three new .vcf files for merge test. By default, there is no merge. Verified that it successfully read three files in the folder and form one BQ Table.
- merge_option_move_to_calls: set variant_merge_stragegy to MOVE_TO_CALLS. Verified that the three files are merged on the keys.
- info_keys_to_move_to_calls_regex: set this field to be "NS" and verified thatthe call.NS value is copied from each VCF file.
- copy_quality_to_calls: set to true. Verified that call.quality is copied from each VCF file.
- copy_filter_to_calls: set to true. Verified that call.filter is copied from each VCF file.

- All the created .vcf files are uploaded to the gcp-variant-transforms-test.
- Integration tests are passed.
Issue: #106

Run Details

3259 of 3611 relevant lines covered (90.25%)

0.9 hits per line

Jobs

ID	Job ID	Ran	Files	Coverage
1	448.1	13 Mar 2018 08:42PM UTC	0	90.25	Travis Job 448.1

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