Published May 18, 2021
| Version v0.25.0
Software
Open
lczech/genesis: genesis v0.25.0
Authors/Creators
- 1. Carnegie Institution for Science
- 2. Cirad
Description
This is a long overdue release that adds a lot of new features, and in particular introduces support for population genetics data, methods, and file formats, and adds an (optional) dependency on htslib.
Important Changes- Add (optional) support for VCF files by wrapping htslib (which now is an optional dependency)
- Add reading support for (m)pileup, GFF/GTF, and PoPoolation2 sync files
- Add tools to work with alleleic variants (SNPs), genome regions, and sliding windows
- Add pool-sequencing variants of population genetic statistics, such as heterozygosity, Theta Watterson, Theta Pi, Tajima's D, and variants of F_ST, by re-implementing methods of PoPoolation and PoPoolation2
- Add filtering and transforming iterator classes
- Add harmonic mean functions
- Add binomial distribution function and binomial coefficient (n choose k) functions
- Add base64 encoding and decoding functions
- Add natural sorting function
- Add simple pure function cache class
- Add svg image embedding and rendering options
- Add simple thread pool class
- Add GzipBlockOutput stream class
- Refactor gzip input stream to work on concatenated gzip streams
- Adapt BmpWriter and SequencePrinter to new OutputTarget classes
- Fix placement sample PqueryName filtering functions
- Fix tree bipartition find subtree function
- Fix bug in tuple hash function
- Fix undefined behaviour in GzipStream destructor
- Bug fixes and speed improvents
Files
lczech/genesis-v0.25.0.zip
Files
(5.2 MB)
| Name | Size | Download all |
|---|---|---|
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md5:17ae60aec64868d80f6b1c91c4fb2a4e
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5.2 MB | Preview Download |
Additional details
Related works
- Is supplement to
- https://github.com/lczech/genesis/tree/v0.25.0 (URL)