0.6.0

update readme

0.5.9

• added consensus flag --consensus only works with odd --top values currently
• standard versioning without v

v0.5.0

• Rust client now available as sketchy -h, main streaming and prediction tasks sketchy stream and sketchy predict
• restructure of the Python client, now as sketchy-utils
• sketchy-utils plot tasks for diagnostic plots
• database inspection and creation sketchy-utils database, making it easier to use a sketch and genotype index to generate custom sketches
• new tasks in the Rust client implementing genomic neighbor typing using Mash algorithms (in addition to streaming function): sketchy screen and sketchy dist
• pull default sketches (S. aureus and K. pneumoniae, s = 1000, k = 15) with sketchy get
• Nextflow workflow for evaluations and bootstrapping in preprint and sketchy-utils integration: collect --> match --> metrics --> plot genotype-heatmap workflow

v0.4.5

• hot fix on watchdog major release removal of has_attribute

v0.4.4

Sketchy v0.4.4

Distribution

• latest versions on Bioconda - thanks to @mbhall88

• Docker container improvements for Nextflow [#46 ]

• S. aureus and K. pneumoniae sketches

• default fast, low resolution sketches (s = 1,000)

• slow, high resolution sketches with sketchy pull --full (s = 10,000)

Modifications

• slightly altered output format to accommodate post processing [#44]
• stability breakpoints now correctly indicate fail to call with -1 [#43]
• removed nested sketch directory structure [#38]
• some minor changes to logging
• change default --ranks to 10 i.e. smaller default consensus window
• renamed break in output to stability to clarify [#39]

Python CLI

• sketchy utils fx-time: extract start time from read headers and link to stability breakpoints

Nextflow

• launching distributed jobs on a cluster is now fairly easy [#46]
• collecting the results as well using sketchy collect [#44]

Example reference panel created with sketchy collect

v0.4.3

• sketches for S. aureus online [#29]
• need more validation data for MTB before inclusion / omission [#29]
• default 15_1000 databases (small, fast, less accurate) [#34]
• full sketches available with sketchy pull --full [#34]
• fixed containers for Docker and Singularity [#34]
• Rust CLI as Cargo package and mobile compute documentation [#35]
• str.strip() behavior resolved [#31]

v0.4.2

Some cleaning up and clarifying code sections. Docker container appropriately implemented. some re-structuring of supporting tasks for feature index construction.

v0.4.1

• fixed critical entry point in setup.py

Rust core in Sketchy v0.4.0

Sketchy rework v0.4.0 - see [#28]

• Rust command line clients sketchy-rs compute and sketchy-rs evaluate for streaming
• Python wrapper sketchy run for convenience to run query - evaluation - plots - pipeline
• Rework of the Python support command line interface sketchy --help
• Feature index file preparation command line tasks to create user-sketches
• Online methods for watching live-runs, simulation in next release
• Singularity and Docker containers, Nextflow pipelines
• Mobile phone application to run Rust client inside VM

Sketchy v0.3-alpha.11

• added Kraken2 section to workflow
• added Kraken2 plots to task sketchy nf-plot