Previously when parsing GAF files, we were relying on there being exactly 1 metadata line at the top of the file (which was an invalid assumption), and furthermore we were not saving the contents of that metadata. With these changes, we capture all lines at the beginning of the file that start with ! and save them in order to be used later during GAF file exporting.
As a consequence of the new StructuredData type from ingest.ts, all of the query functions now simply accept the StructuredData object rather than passing multiple data objects (e.g. geneMap and annotations) to every function call.
Previously when parsing GAF files, we were relying on there being exactly 1 metadata line at the top of the file (which was an invalid assumption), and furthermore we were not saving the contents of that metadata. With these changes, we capture all lines at the beginning of the file that start with
!and save them in order to be used later during GAF file exporting.As a consequence of the new
StructuredDatatype fromingest.ts, all of the query functions now simply accept the StructuredData object rather than passing multiple data objects (e.g. geneMap and annotations) to every function call.