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Draft reader/codec factory draft - WIP. #51

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@cmnbroad cmnbroad commented Mar 4, 2019

This isn't ready for line-by-line review; more just for discussion at the next meeting.

Draft implementation of a dynamic HtsjdkCodec discovery and registration service, implemented via a java.util.ServiceLoader. Each HtsjdkCodec consists of two classes; a lightweight, dynamically discovered singleton HtsjdkCodecDescriptor, which is cached in a registry, and the actual HtsjdkCodec itself, which is only instantiated with actual inputs when the corresponding HtsjdkCodecDescriptor claims to be able to handle a given input resource.
This PR contains a single stub/mock BAMCodec implementation as a test case for exercising the discovery/registry code.

This does not include any changes discussed during the last meeting(s). In particular:

  • we still need to define an additional service layer for use by codecs to map/resolve input resources to actual consumable channel/stream/resources
  • a way to provide sibling file indentifiers directly

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