Martin Pollard
Martin Pollard
The thing is there already is a defined way to escape these characters in the VCF specification the % encoding as I mentioned above, there's no need to make a...
Actually scratch that, it looks like you're doing a lot of raw VCF handling yourselves so you might need to do the escaping too?
I can confirm that the same data under Python 3.10.1 works so def some 3.11 oddity for your list.
I've now managed to replicate this converting that cram to a bam with samtools proper so I'm raising this with the samtools team.
It's a funny one, and kinda low level so you probably can't catch it. I got James Bonfield to have a look at the CRAM and he found the problem,...
Bug fix for htslib is in: samtools/htslib#1613. I'm going to ask Rob if we can make a release soon.
Any chance this could be merged? Python2 is rather dead and this is still a useful tool
So interestingly I haven't retested this on my new Grace Hopper (Ubuntu 22.04.4 LTS) until today (previous testing was done on a remote system). I no longer get the original...
I have replicated this, The issue seems to be with: ``` # check for multiple AFs in snv if type(snv[self.af_tag]) == tuple: ``` which is defined in the header by...
This has now been tested on UK10K cohort BAMs and in combination with a correction to samtools fixmates has resolved the problem we had with orphaned paired reads (which had...