Jeremiah Wala

I can’t see the whole SV, but if is a discordant-read only SV (DSCRD), it won’t be in alignments (contigs) file. On Mon, Jul 31, 2023 at 10:30 AM hhd1008611...

well the discordant reads are relevant for CNVs. What I think you mean is that they aren't substantial contributors to the copy-number. Svaba aims to compile rearrangement breakpoints, especially complex...

I think the issues are now related just to `refilter`, which was a sort of back-end convenience function I used at one point. To keep the maintenance simpler I've decided...

It seems that would mean that this was supported by only discordant reads. Depends on your library — if it is low-coverage large-insert size (like a mate pair library) then...

This is more odd, but I suppose could be explained by the 2nd issue with SVs in that the read depth could be defined at *either* breakpoint A or breakpoint...

@ahwanpandey This is one the memory/run weakness of svaba that I've known about but haven't had time to fix. The issue is that svaba compiles all of the variants into...

Hmm OK, I'm concerned given that file size of bps.txt.gz (not so big) that there is a memory clash happening somewhere that's running up the memory as a bug. There...

This is fixed in the latest commit (`d9f37dbc40ed783b5758389405113ac2a0dfbd82`)

Missing `#include SeqLib/RefGenome.h`

A suggestion would be to check the config.log and see where it is failing. configure will try to build a test program when checking for these headers and libraries, and...