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Only some trips are grouped into routes in our feed. The raw dataset we generate the GTFS feed from doesn't really have anything that maps to the concept of "routes" in GTFS. Since GTFS discourages, but allows even the extreme case of a 1:1 relationship between trips and routes, we chose to only group trips into routes where the raw data also does it. This makes for a slightly bigger dataset, but prevents possibly wrong interpretations of the raw data by an automatic grouping.
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PS: the documentation (only available in german) describes the route id generation in detail.
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Thanks a lot for the explanation, perhaps you would be interested to take a look at the GTFS data released by SBB recently (they also do some conversion from HAFAS):
https://opentransportdata.swiss/en/dataset/timetable-2017-gtfs
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