d4-format
d4-format copied to clipboard
38
The D4 Quantitative Data Format
Using "D4 Utilities Program 0.3.7" installed with conda I created 3 d4 files using different mapping quality filters: d4tools create --mapping-qual 0 S01_HyperPlus_Program1_HyperExomev1_Rep1_S1_sorted_dupsrm.bam MQ0.d4 d4tools create --mapping-qual 20 S01_HyperPlus_Program1_HyperExomev1_Rep1_S1_sorted_dupsrm.bam MQ20.d4...
I've noticed that some crams/bams seem to result in empty d4 files. I'm not quite sure why. An example are the HGDP cram files (e.g. ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/HGDP/data/Yi/HGDP01180/alignment/HGDP01180.alt_bwamem_GRCh38DH.20181023.Yi.cram). I can even subset...
Hello, Would it be possible to implement simple median coverage stats for a selected region? While one can get the data using i.e. ```d4tools view input.bam 22:39349000-39349100``` there is "some...
pyd4 is available as a python package, but only as a source distribution, requiring a rust compiler to install---which is still a rare find on hosts to Python. After a...
It looks like the base image for rust is too old. https://github.com/38/d4-format/blob/151f27cb06a32880f7e8d6e256b94d60361adf32/Dockerfile#L1 Changing `FROM rust:1.50 as builder` to `FROM rust:latest as builder` results in a mismatched types error: ``` #11...
Currently, the `view` command will accept a list of regions in ... format on the CL. It would be a nice addition to allow a BED file to be specified...
Dear @38 , Thank you for developing d4tools. When I compile the latest version (0.3.2), I constantly got a missing header error (bzlib.h), then I looked into build_htslib.sh, if we...
Hi, I was interested in using d4utils on combination with modepth, but I am not sure if I should build for source, or use the binary in the release, which...
for example, i'd like to turn on deflate and set the level.
I've just run into an annoying issue building on a system where I lack `sudo`. While compiling locally with `cross` is possible for me, it would be great if folks...
