Matthias De Smet

I'll compile from source and give you an update shortly. Thanks M

I can confirm the fixes in the `bug_fixes` branch *do not* fix this issue. The process still crashes with `(ERR): bowtie2-align exited with value 139`. This occurs regardless of using...

Apologies. It seems the alignments do work when using unaligned bam files. When using an aligned bam file, the segfault occurs. Would it be possible to just ignore the offending...

Hi, Sadly, I'm not allowed to share any data from our work.

Hi @ch4rr0 , I'm not really sure that's the desired outcome. If I'm not mistaken, this would only attempt to align the unmapped reads, while skipping all the rest. I...

Hi @ch4rr0 Any idea when we can expect a new release with the fixes for this issue? Thanks M

I must note `bwa` has the same issue

Hi, Thanks for the quick reply and fix! Looks great 😄 Now just to nitpick a bit, but do you suppose it makes sense to keep the read/filtered/control number info...

Hi, Apologies, it seems the error was on my part. As you stated, all tags are transferred neatly to the aligned bam. Would there be a possibility to add the...

Sure, here's an excerpt with the 10 first variants from that file. [tmp.vcf.txt](https://github.com/brentp/cyvcf2/files/8370391/tmp.vcf.txt)