Jacob Munro

terminate called after throwing an instance of 'std::runtime_error'

8

**Issue description:** raxml-ng fails on certain input for an unknown reason. The time until failure seems to depend on the random seed used. Jobs have been run on an HPC...

lumpy_filter slower with 2 threads than 1

2

The lumpy_filter command used by `smoove call` uses 2 threads, regardless of the `--processes` argument given to `smoove call`. Observing the running processes shows around 5-10% cpu utilisation. Testing the...

Generally VCF files are accompanied by an index file, and from this file the number of variants can be obtained. For example with bcftools: `bcftools index --nrecords ` This could...

It would be useful to be able to optionally set the launch directory to be unique from the pipeline launch interface. This would avoid potential file name collisions resulting from...

Feature suggestion: It would be great to have an option to treat reads with zero length the same as missing reads. These reads come up from time to time in...

"dry run" option?

15

When using the -resume option, it would be helpful to see which processes are going to be run and which will be reused from the cache. Additionally it would be...