multiple mapping

[yjk-bertrand]

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]

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

[JianjunJin]

@yjk-bertrand Are you having a similar experience like this #78 ?