Benjamin Redelings

I was able to reproduce the bug and figure out where it is coming from.

I've fixed the testsuite error on the `master` branch. I'm planning to do a new beta9 release at the end of January, which would include the fix. I'm aiming to...

Hi Andreas, I finally did a beta9 release, so the issue should be fixed. Would you be able to build beta9 for experimental? -BenRI

Hi Andreas, Would you be able to build beta13 for experimental? -BenRI

:grimacing: Ah, yes, now that I have fixed the ref.vg file, it gets further. However, now it looks like `char CommonUtils::Complement(char)` has an assertion that fails. Although `assert(false)` is not...

Actually, I had put some `=` characters in between contigs. After I removed them, it is running fine.

It seems that if the input file is called "a", then no sequences are read in. However, if it is called "a.fasta" then sequences are read.

It has almost worked, but there is also this error: ``` ERR2679010-2x-LT635612 LT635612 seed 30145/30148 3653+,759490,20,10 skipped (overlap) ERR2679010-2x-LT635612 LT635612 seed 30146/30148 24396+,640231,20,9 skipped (overlap) ERR2679010-2x-LT635612 LT635612 seed 30147/30148 23047+,281879,20,8...

Here are some files: [plaf.txt](https://github.com/DEploid-dev/DEploid/files/5896286/plaf.txt) [ERR2678989.vcf.txt](https://github.com/DEploid-dev/DEploid/files/5896291/ERR2678989.vcf.txt)

I modified the utilities scripts locally to convert `.` to `0`, similar to the PR for DEploid itself. Octopus writes VCFs with `.` when there is no haplotype that covers...