Marco Mariotti

Hi @Zulko @veghp, thanks for developing this package. I write just to strongly encourage you to develop this feature (display grouped connected exon structures, as in the image shared by...

Hi, get_sequence uses pyfaidx under the hood. What happens is that the fasta file is indexed if an index (.fai) is not found, then the index is used to fetch...

In our hands, pyranges extracting sequences from annotations is correct. Our lab uses this function very often. Let's get to the bottom of this. Please paste a link to the...

@brian-arnold can you provide data to replicate the error? Otherwise we'll have to close the issue thanks!

This issue has increased priority now. As soon as we have enough workforce we'll address it. Some thoughts on the way forward: - create a simple VCF/BCF reader (or rely...

@endrebak I think this is done already, can you confirm? Can we close the issue?

This is an interesting problem for which we should add support. In general, methods that accept a "other" PyRanges shrink it to the minimum because its information may not align...

Endre's solution is the right one. I'll extend it here: ``` signal_data = pr.data.chipseq() # make up some ints, or it's all zeros, not great as example signal_data.Score = np.random.randint(0,...

This issue is still present, as bioconda installs version 0.0.3 of sorted_nearest. As consequence, today on a clean pyranges installation, some methods fail, e.g. _max_disjoint_

New documentation available at https://pyranges.readthedocs.io/