Jeremiah Wala
Jeremiah Wala
This BAM header has 3366 sequence tags as svaba reports, so I don't see an issue here. You'll have to confirm how many sequences the reference fasta has. On Tue,...
I still think the reference and the header are different. @zhaowsong can you confirm with `grep` etc the number of unique reference contigs in both the reference and the bam...
I don't know! The default constructor for the object that holds the breakpoints has a value of `0`, but I don't know why this wouldn't always be set in the...
you may want to set `--max-reads` to `0` to turn off read capping
Yes this is a problem with GCC 10+ and the fml subdirectory. I'm working now on refactoring SeqLib to point to more modern versions of these repositories (where this problem...
oops @tnnandi, I forgot this was the svaba github, so SeqLib is a subdirectory itself of svaba. So you would `make` from the svaba main directory, not the SeqLib subdirectory...
> Hi @walaj, > > If it's any help, I've made these fixes in my forked branch: https://github.com/julianhess/SeqLib/commits/jhess > > Apologies for not PR'ing this years(!) ago. > > —Julian...
Ahh so you'll need to also change the remote of the fermi-lite directory. In fermi-lite: `git remote set-url origin https://github.com/lh3/fermi-lite` `git fetch origin` `git reset --hard origin/master` You can confirm...
This is an issue with the conda environment not having the header files for the version of bzip2 that you installed. This worked for me: `conda install -c conda-forge bzip2`...
Doesn't the command with `-m 100` set max coverage to 100, not 50?