Tom Conway
Tom Conway
In case it helps, I have a Streams API wrapper, which I modified to support the multiple streams in a file. This supports both regular gzipped files, and bgzip ones....
Here's a stand-alone HTML document. Select a file - it uses suffix matching to guess if it's compressed or uncompressed, and it reads the chunks. ```html Uncompress Streams // Define...
Hmm. I changed the version of pako that I was using from 1.0.3 to 2.0.4 and it fails now. Is there an obvious thing that changed that would break the...
I had the same problem, and this solution worked for me. https://github.com/rust-lang/flate2-rs/issues/339
There are obviously pros and cons in enforcing the restricted vocabulary. I note that as things stand, you can't use the noodles library to write a program to correct well...
Reflecting some direct emails, there seem to be some examples where the alignments have slightly odd indel behaviour, where `bwa` is happy to soft clip. I made a recipe for...
I don't have much experience with single cell data (genomic or RNASeq), but it sounds to me like there could be some step in the library preparation that biases toward...
I'll have to consult - as I indicated, it's a clinical sample. The smallest expansion would be to track `RefCall` entries, either by adding to the tuple in the set,...
Unfortunately, I can't give you a BAM with the reads.
Just to update - we have found more instances of this problem. Unfortunately in clinical samples that we can't share. It's a significant problem for us, because in trios, it...