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maickrau / GraphAligner

MIT License
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GfaGraph.cpp assertion failed when loading recent VG based GFA #37

Closed brianabernathy closed 3 years ago

brianabernathy commented 3 years ago

I've noticed a recent change in GFA graphs produced by VG. Previously, the path record overlaps field contained segment lengths and link record overlaps were set to '0M'. Recent versions of VG now produce path and link overlaps of '*'. This results in the error below when running GraphAligner.

GraphAligner: src/GfaGraph.cpp:271: static GfaGraph GfaGraph::LoadFromStream(std::istream&, bool, bool): Assertion `dummyc == 'M' || (dummyc == 'S' && overlap == 0)' failed.

If I manually set GFA link record overlaps to '0M', GraphAligner parses the file successfully.

maickrau commented 3 years ago

Starting with commit cc4562c GraphAligner will now assume that overlaps of "*" are "0M"

brianabernathy commented 3 years ago

Great, thanks for the quick fix.