Ruben Vorderman
Ruben Vorderman
I added the ability for `dnaio.open` to open multiple files. I also added the `dnaio.open_multiple` API which iworks in case you want 1-tuples for 1 file. (I use this sort...
A while ago I watched some videos on optimization and having a look at generated assembly code. Since dnaio is a relatively straightforward project. I decided to have a go...
Currently I am working a lot with UMI data that is stored in a separate FASTQ file meaning I have 3 files now. I needed to filter those files on...
Currently dnaio uses a slightly unusual architecure where the first value of fastq_iter is a boolean, not a SequenceRecord. This determines whether all coming fastq headers are printed with two...
### Version of Singularity: 3.5.3 ### Expected behavior ``` $ singularity exec --containall docker://quay.io/biocontainers/fastqc@sha256:319b8d4eca0fc0367d192941f221f7fcd29a6b96996c63cbf8931dbb66e53348 fastqc --version FastQC v0.11.9 ``` This will pull the image at the correct sha256 hash. If...
The [Intel Storage Acceleration Library](https://github.com/intel/isa-l) is an implementation of the DEFLATE algorithm **written in assembly**. As a result it is very fast. It can be used as a replacement for...
The newest version of the BWA kit archives posted here (https://sourceforge.net/projects/bio-bwa/files/bwakit/) still uses an older version of BWA (0.7.15). Since I prefer to fix problems instead of complaining I tried...
The CopyWorkflowActor regularly gets timeouts when trying to copy the gigabytes of data that are typically associated with production workflows. Also this duplicates the amount of disk space used for...
The [Intel Storage Acceleration Library](https://github.com/intel/isa-l) provides very fast zlib-compatible compression and also very fast CRC calculation. Speed ups from 3-6x are not uncommon in the decompression/compression department. Despite the name...
XXH3 and XXH3_128 are now stable since [XXHash release 0.8.0](https://github.com/Cyan4973/xxHash/releases/tag/v0.8.0). They perform even faster than XXH64 which is quite remarkable. It would be nice if these were available from lz4-java,...