d4-format
d4-format copied to clipboard
38
The D4 Quantitative Data Format
ENCODE folks suggested this was a need. What are the current bottlenecks? Speed? ANalytical flexibility?
Hi @38 and @arq5x, I am getting an error when trying to open a d4 matrix in pyd4: ``` OSError: memory map must have a non-zero length ``` I have...
Hi, I want to look at the mean expression over a number of regions defined in a BED file. Currently using `d4tools stat` with `--region` output the mean for each...
Hi, I am trying to use `d4tools view` on my d4 file but don't get any output. I am using the command as below. ``` $ d4tools show --region-file tmp.bed...
Hi, thanks for a great tool! I'm seeing some issues in a d4 file (created with `d4tools create -A basecalls.bam basecalls.d4`). There appear to be large flat regions in the...
There is an issue with libc on aarch64, in that it has c_char aliased to u8, whereas on amd64 libc uses i8 for c_char. The result of this is that...
Hi, I'm running variant calling on non-model organisms, and for some of the downstream analyses (e.g., nucleotide diversity calculations), it is necessary to generate (possibly boolean) accessibility masks that classify...
This is something we are looking at over at the https://github.com/Clinical-Genomics/chanjo2 repo. The current approach is to read the output from the d4 file using `d4tools show`. It would be...
Leaving this for reference. Working with #78, I also tried running indexed d4 files. Here, I also got strange results. I traced it in the code, and did not seem...
I'll make a genome of 30 bases, and my BAM has one read, 21 bases in length, that spans from bases 5-25 (1-based start) or 4-25 (0-based start): ``` ██████FAKE_READ██████...
