Closed adamnovak closed 3 months ago
Robin reported a crash in https://ucsc-gi.slack.com/archives/CJ2EHEH1A/p1719441485497449 where we fail an assert in the alignment emitter about having the same number of alignments for each read, when emitting paired reads.
If we hit this fallback code here: https://github.com/vgteam/vg/blob/5bc8f8a55f682d826d5276ae502e4cf6743d68b3/src/minimizer_mapper.cpp#L1352-L1369 Then when multi-mapping (-M > 1) is on, we can end up with different numbers of alignments for each read.
-M
We need to add code to make syntactically valid pairs even when we have no distribution to guide how to pair the reads up.
Robin reported a crash in https://ucsc-gi.slack.com/archives/CJ2EHEH1A/p1719441485497449 where we fail an assert in the alignment emitter about having the same number of alignments for each read, when emitting paired reads.
If we hit this fallback code here: https://github.com/vgteam/vg/blob/5bc8f8a55f682d826d5276ae502e4cf6743d68b3/src/minimizer_mapper.cpp#L1352-L1369 Then when multi-mapping (
-M> 1) is on, we can end up with different numbers of alignments for each read.We need to add code to make syntactically valid pairs even when we have no distribution to guide how to pair the reads up.