cathoderaymission

Fix for "Not enough space"

2

In ctcdecode/src/binding.cpp change: `const char* end = str_i + strlen(labels)-1;` to `const char* end = str_i + strlen(labels);` I'd submit a patch, but I'm not 100% sure about the utf-8...

``` vocab = ["A", "B", "C", "D", " "] decoder = CTCBeamDecoder(vocab, beam_width=5, blank_id=vocab.index(' '), log_probs_input=True) decoder.decode(out) py3/lib/python3.7/site-packages/ctcdecode/__init__.py in decode(self, probs, seq_lens) 38 ctc_decode.paddle_beam_decode(probs, seq_lens, self._labels, self._num_labels, self._beam_width, self._num_processes, 39...

What happens when nanopolish model_kmer is NNNNN?

1

Looking at the code for xpore 2.0, I can see the following: ```assert list(set(g_kmer_array))[0].count('N') == 0 ##to weed out the mapped kmers from tx_seq that contain 'N', which is not...

xpore processing of Epinano Yeast fails

10

I downloaded and am using the latest xpore 2.0 release off github. 1. Basecalled all 3 replicates of each of the WT and KO Yeast SK1 from the epinano paper....

Per issue #73, an issue for a feature request to report on the methylation status and location for individual nanopore reads.

Per issue #73, a new issue to request support of GFF files as GTF files are older and GFF3 has been a standard for awhule.