Marcus Stoiber
Marcus Stoiber
I've experienced a memory leak when using the python `mappy.Aligner` when initialized with a sequence file/FASTA (this is within [Megalodon](https://github.com/nanoporetech/megalodon)). This same memory leak does not occur when the `Aligner`...
I have just come across this behavior testing out mappy on a genome file that I had accidentally moved. `mappy.Aligner` is able to initialize with a non-existent file, but any...
This project looks very promising. Is it possible/are there plans to provided a python interface (`winnowmappy`) to this software? For some more detail, I am the developer of the Oxford...
New subcommand to identify regions with heterozygous bases. Should be some type of multimodal versus unimodal test. Will also have to filter out off-by-one regions, maybe by offset testing.
Create an index file when running genome_resquiggle that is linked to directories and loaded instead of querying all files for all subsequent commands. This should essentially be the parsed files...
Both the plot_motif_centered and plot_motif_with_stats subcommands do not correctly handle strands. plot_motif_centered only searches the forward strand. The plot_motif_with_stats subcommand only prints regions from the forward strand and stats need...
This will use many of the functions from the plot_signal script. This is probably just a list of the mean and sd of corrected events in an HDF5 format array....
User should be able to provide blacklist regions for largest difference, most significant or other region selection criterion.
Create a kmer model from corrected signal. Would allow identification of bases that deviate from a kmer model.
There is a check in the code that the version of matplotlib is great than 3.7 for a particular feature [here in the code](https://github.com/ponnhide/patchworklib/blob/235bfbc9fa5c43b5386ba247f438ff622d22858c/patchworklib/patchworklib.py#L176). This is currently completed with a...