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BrendelGroup / AEGeAn

Integrated toolkit for analysis and evaluation of annotated genomes
http://brendelgroup.github.io/AEGeAn
ISC License
24 stars 10 forks source link

Better use of GtNodeStream classes #55

Closed standage closed 11 years ago

standage commented 11 years ago

The GtNodeStream provides a nice solution for processing annotation data while loading it into memory and/or writing it to disk. AEGeAn does not yet utilize this interface, but it has a lot to gain by doing so.

standage commented 11 years ago

Potentially useful: GtSortStream, GtExtractFeatureStream, GtVisitorStream. Have similar functionality to AEGeAn core code but probably cannot be used: GtAddIntronsStream, GtInterFeatureStream, and GtMergeFeatureStream. Also potentially useful: GtGFF3Visitor.

standage commented 11 years ago

Commit a08675d08315cfffbfe26b2e9cdd1cb6d495660f makes the initial attempt to convert from the old agn_import_canonical to a new entirely stream-based importing method. This did indeed utilize the AgnAddIntronsStream (and of course several others). Subsequent refactoring slated for most input / output tasks.

standage commented 11 years ago

Huge strides have been made as of commit c358316ab58c8c0d5ba5c58b3668e888241467af, and for all intents and purposes this issue is now closed.