There is a newer version of the record available.

Published May 18, 2021 | Version v0.25.0

lczech/genesis: genesis v0.25.0

  • 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
Notable Changes
  • 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
md5:17ae60aec64868d80f6b1c91c4fb2a4e
5.2 MB Preview Download

Additional details

Related works