direct-io
MMseqs2
direct-io | MMseqs2 | |
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1 | 4 | |
66 | 1,259 | |
- | 1.9% | |
0.0 | 7.7 | |
about 1 year ago | 5 days ago | |
C | C | |
MIT License | GNU General Public License v3.0 only |
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direct-io
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But How, Do Databases Use Mmap?
I wrote this for Node.js, which is a native binding in C, exposing cross platform functionality: https://github.com/ronomon/direct-io
Although if it's a new project and you're used to C, I would recommend also taking a good look at Zig (https://ziglang.org/), because it's so explicit about alignment compared to C, and makes alignment a first-class part of the type system, see this other comment of mine that goes into more detail: https://news.ycombinator.com/item?id=25801542
Something that will also help, is setting your minimum IO unit to 4096 bytes, the Advanced Format sector size, because then your Direct IO system will just work, regardless of whether sysadmins swap disks of different sector sizes from underneath you. For example, a minimum sector size of 4096 bytes will work not only for newer AF disks but also for any 512 byte sector disks.
Lastly, Direct IO is actually more a property of the file system, not necessarily the OS (e.g. Linux), so you will some file systems on Linux that return EINVAL when you try to open a file descriptor with O_DIRECT, simply because they don't support O_DIRECT (e.g. a macOS volume accessed from within a Linux VM) so that should be your way of testing for support, not only the OS.
MMseqs2
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Clustering tool that could help cluster protein sequences based on percentage identity
A tool I often recommend for sequence clustering is mmseqs2 : https://github.com/soedinglab/MMseqs2, fast and efficient :)
- MMseqs2 – an example of great software for biology
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Metagenomics: abundances of short reads using genome databases
Tools like the the mmseqs2 "taxonomy" module, or DIAMOND v2, can efficiently align contigs to genome databases to assign taxonomy, but it seems like they aren't intended to provide abundance estimates for each taxon (since that would require mapping reads, and mmseqs2 can't even use paired-reads). Can anyone recommend tools or methods for A) connecting per-contig coverage information to contig taxonomy, or B) mapping short reads against genome databases?
- Retrieving One-to-One Orthologs of Unprocessed cDNAs
What are some alternatives?
httpdirfs - A filesystem which allows you to mount HTTP directory listings or a single file, with a permanent cache. Now with Airsonic / Subsonic support!
kraken-biom - Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).
imdb-rename - A command line tool to rename media files based on titles from IMDb.
samtools - Tools (written in C using htslib) for manipulating next-generation sequencing data