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maickrau / GraphAligner

MIT License
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multiple mapping #96

Open yjk-bertrand opened 9 months ago

yjk-bertrand commented 9 months ago

I am using a blunted assembly graph from short reads that contains several paralogs. I am aligning a long read to the graph that should partially match several paths on the graph. I have tried several combinations of --multimap-score-fraction values. Yet, graphaligner always outputs a single mapping for the query. Is there a way to get every mapping, even the partial ones?

maickrau commented 2 weeks ago

Using --multimap-score-fraction 0 should prevent it from discarding alignments as secondary. If this doesn't work then could you upload a test graph and read where the secondary alignments are missing