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googlegenomics / dataflow-java

Google Cloud Dataflow pipelines such as Identity-By-State as well as useful utility classes.
Apache License 2.0
36 stars 31 forks source link

Rearrange code. #180

Closed deflaux closed 8 years ago

deflaux commented 8 years ago

Pipeline-specific functions were pushed down a package level and one reusable function was moved out of an obsolete 'grpc' package level.

@iliat please take a look at the new organization and let me know if any of the BAM stuff should be grouped differently.

https://github.com/deflaux/dataflow-java/tree/rearrange/src/main/java/com/google/cloud/genomics/dataflow/functions

https://github.com/deflaux/dataflow-java/tree/rearrange/src/main/java/com/google/cloud/genomics/dataflow/utils

https://github.com/deflaux/dataflow-java/tree/rearrange/src/main/java/com/google/cloud/genomics/dataflow/writers/bam

coveralls commented 8 years ago

Coverage Status

Coverage remained the same at 20.263% when pulling efdf35f058e2b9baffe07ec3ac405bbde1573546 on deflaux:rearrange into 7d25de2f8be3428ff12dc8f57a967f000d804a15 on googlegenomics:master.

pgrosu commented 8 years ago

I would use more general terms such as analysis, validation or qc to group a larger set of classes under. It would be hard for folks to remember transmissionprob as package names, as in Java either they have the whole name in CamelCase, or is only one common word that is truncated, or has the whole package name as an acronym.

The Java class hierarchy provides a nice idea of how to structure an API:

https://docs.oracle.com/javase/8/docs/api/java/lang/package-tree.html

https://docs.oracle.com/javase/8/docs/api/java/util/package-tree.html

Hope it helps, ~p

iliat commented 8 years ago

LGTM for BAM, Thanks !

coveralls commented 8 years ago

Coverage Status

Coverage remained the same at 20.263% when pulling 8b0661044b5feb116e5872a0cdb6f6212089525b on deflaux:rearrange into 7d25de2f8be3428ff12dc8f57a967f000d804a15 on googlegenomics:master.

coveralls commented 8 years ago

Coverage Status

Coverage remained the same at 20.263% when pulling 1b92fb6754c705a3d4b602cf5434179de940855a on deflaux:rearrange into 7d25de2f8be3428ff12dc8f57a967f000d804a15 on googlegenomics:master.

pgrosu commented 8 years ago

The fixes look nice - thanks Nicole :)

coveralls commented 8 years ago

Coverage Status

Coverage remained the same at 20.263% when pulling 0134a4fcd15c082b0929e9d0015f8dae0673fcfb on deflaux:rearrange into 7d25de2f8be3428ff12dc8f57a967f000d804a15 on googlegenomics:master.