svtools
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hall-lab
Tools for processing and analyzing structural variants.
Hi, I have found several examples where a deletion (or duplication) is detected within a region that has already been deleted according to another event. For example, take (1) and...
Hi! I'm trying to understand the difference between ++ and -- strandedness in BND's with both break-ends on the same chromosome. From [here](https://github.com/hall-lab/svtools/issues/104) I understand that these are one-sided inversions....
It doesn't seem like it needs to. Currently loads the entire bFile into memory. This could be fixed by requiring sorted files.
Lots of repetitive code exists in and around parsing headers etc for these formats. Abstract into reader and writer classes.
Currently this is only used by prune
These are basically the same script but with different sort parameters. Collapse into one and set the sort from the command-line.
Especially for numpy, pandas, scipy, statsmodels...
This is a bottleneck step and currently runs in ~45 minutes per genome
Fix lmerge to do what we actually want it to, and we may be able to eliminate prune step, which is a bit clunky.
This option wasn't functional, but we do want it to add in the confidence intervals as they aren't output by certain tools.