James Ferguson
James Ferguson
No NULL catch in the file open steps to raise a memory error causes seg fault ``` if self.state == 0: self.s5 = pyslow5.slow5_open(self.p, self.m) >>> insert NULL check here
The min qscores used for various models is stored in the .cfg files I should extract them when using the `--config` arg. Need to investigate if that info is stored...
Add FAQ eel hangs if bin path and lib don't match info about args passed to dorado-server not in --help (find a way to add them to help maybe?) info...
with the changes in how dorado-server processes batches, it is causing performance issues. I need to change the current static pipeline of ``` 1. get batch 2. mutate batch into...
Hey, I'm trying to figure out what the inteded best method of writing data to a pod5 file is. The API has the `vbz_compress_signal_chunked()` step that does the compression, then...
Hello, I see arrow has methods for converting between endianess and the write_footer() looks like it should handle big or little https://github.com/nanoporetech/pod5-file-format/blob/2b2c29f01e3e6c80c4028edacbc0500235c00001/c%2B%2B/pod5_format/internal/combined_file_utils.h#L128 Just wondering if there is full compatibility? There...
python3.9 goes EOL soon. Need to bump minimum python up to 3.10
Move the testing scripts to use a newer 5khz model and data. make sure all tests pass handle any output differences
Before this change https://github.com/samtools/htslib/pull/1854 U was changed to N when read by samtools Now it will be changed to T However, I think it would be "better" if we could...
Currently, the sam spec document (https://samtools.github.io/hts-specs/SAMv1.pdf) has the following for the mandatory SEQ field 10 SEQ String \*|[A-Za-z=.]+ segment SEQuence  This doesn't really match up with the IUPAC base...