adam
uvfs
| adam | uvfs | |
|---|---|---|
| 3 | 3 | |
| 967 | 5 | |
| 0.2% | - | |
| 6.1 | 0.0 | |
| about 1 month ago | almost 2 years ago | |
| Scala | C++ | |
| Apache License 2.0 | GNU General Public License v3.0 or later |
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adam
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biobear -- python package with minimal dependencies for bioinformatic file parsing and querying using rust and polars as the backend
FYI: ADAM seems to do that
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Advanced Scientific Data Format
We presented using Parquet formats for bioinformatics 2012/13-ish at the Bioinformatics Open Source Conference (BOSC) and got laughed out of the place.
While using Apache Spark for bioinformatics [0] never really took off, I still think Parquet formats for bioinformatics [1] is a good idea, especially with DuckDB, Apache Arrow, etc. supporting Parquet out of the box.
0 - https://github.com/bigdatagenomics/adam
1 - https://github.com/bigdatagenomics/bdg-formats
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Seq: A programming language for high-performance computational genomics
We're here, still plugging along.
ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.
https://github.com/bigdatagenomics/adam
uvfs
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C++ Show and Tell - October 2022
recently I had the need for an archive format where file access could be mmap'd and with very fast random access to the contained files. not sure if I managed but if that can be useful to anyone: https://github.com/celtera/uvfs ; ideally i'd like to investigate how to serialize the hash map directly so that it could just be mapped too instead of having to recreate it on load.
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Advanced Scientific Data Format
I had started a little bit of work towards that recently: https://github.com/celtera/uvfs
It's very optimized towards my specific needs but could be a basis for what you mention
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DwarFS: The SquashFS successor has arrived
ended up biting the bullet and started https://github.com/celtera/uvfs
What are some alternatives?
seq - A high-performance, Pythonic language for bioinformatics
asdf - ASDF (Advanced Scientific Data Format) is a next generation interchange format for scientific data
bioconda-recipes - Conda recipes for the bioconda channel.
hwinfo - cross platform C++ library for hardware information (CPU, RAM, GPU, ...)
nimconf2021 - Slides for Nimconf21
DataContainer
BFScript - A compiler backend paired with a proof of concept programming language that compiles to Brainfuck.
cramino - A *fast* tool for BAM/CRAM quality evaluation, intended for long reads
Pepper - PE32 (x86) and PE32+ (x64) binaries analysis tool, resources viewer/extractor.
sito - sito: A serialization suite
CustomKeyboard - A swiss knife for myself - automotive development tools and a plenty of other things