Add a pipeline that loads BAM into BigQuery

googlegenomics / dataflow-java

Google Cloud Dataflow pipelines such as Identity-By-State as well as useful utility classes.

Apache License 2.0

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Add a pipeline that loads BAM into BigQuery #220

Closed nmousavi closed 5 years ago

nmousavi commented 5 years ago

Tested on Dataflow as well as local

nmousavi-test:bam2bq_test.dataflow_java nmousavi-test:bam2bq_test.dataflow_java_1

nmousavi commented 5 years ago

Travis failure msg:

"The job exceeded the maximum log length, and has been terminated."

https://api.travis-ci.org/v3/job/452491343/log.txt

coveralls commented 5 years ago

Coverage decreased (-0.9%) to 20.626% when pulling aa44cde20e8f2257a95e3273be8b1a5829dccee9 on nmousavi:bq-import into 4f94f80d18a7b6ccca9c15a65e31d0db3231b887 on googlegenomics:master.

nmousavi commented 5 years ago

PTAL!