genegolts

It's v. 2.0.2

Just ran it. It outputs reads identical to my inputs. Thanks for looking into this!

Just to add visuals to the story, here's a slide describing the problem. 

Pulled commit 3f1e664 and re-built the target. Still getting the same unevenly clipped consensus pair. Would it help if I uploaded the mini-bam file I'm testing this on?

@mjhipp Thank you for the explanation, it makes perfect sense. In my use case scenario, this behavior results in the sequence at chimeric or fusion breakpoints getting hard-clipped. I can...

It's v. 2.0.2 On Mon, Apr 25, 2022 at 1:30 PM Nils Homer ***@***.***> wrote: > @genegolts what version of fgbio are you > using? There was some behavior difference...

Hello again. One common use case for consensus reads is to detect "split alignments" as a sign of structural variation in a genome, and in this scenario you would absolutely...

Thanks you for adding the solution here. It would really help if this was also in the README.

Experiencing the same problem in version 4.8.1. The fasta output is not sorted by cluster size, with or without -sf 1.