Eric T. Dawson
Eric T. Dawson
Adds the necessary functions for outputting the chains of anchors that represent an overlap.
This PR brings in filtering strategies that mimic those of minimap2. - [X] Self mappings: minimap2 does not output self mappings (where an overlap between a read and itself covers...
In theory, this branch will help push our accuracy closer to that of minimap2 through changes in the chaining and scoring algorithms. It also includes some filtering improvements (which may...
Despite updating the evaluate_paf script to handle queries better, the performance of the script is inadequate for large-scale CI jobs. One solution to this is to ditch the interval tree...
Currently, the evaluate_paf script in pygenomeworks (and the backing readers) require input to be raw text. However, we often use gzip-compressed PAF to save space, and miniasm natively supports reading...
The GFA specs state that overlaps for `L` lines are optional, but minigraph seems to require these. I think this happens because there is no way to avoid parsing a...
When passing a list of INFO fields and reading a VCF region where no variants have an entry for the field, an error is thrown. This happens with the 1000...
When reading a VCF and parsing a specific region, the reader can crash if that region contains no variants. This can happen if the region is truly empty or if...
I have a relatively small (34MB) graph that when attempting to index uses over 16GB of RAM and is subsequently killed on my machine. @ekg thinks this may be caused...
Hi @brentp , While testing this, I noticed that it's possible to pass `-B ` at the command line and override the `-B 2` value set in `bwa-meth.py`. Is this...