v1.1.2

Minor release after a couple of patches. Main changes:

• better indexing and serialisation strategy - results in much smaller files
• code has been cleaned up to remove unused packages - e.g. old LSH Forest code
• fixed a data race that occurs when a read maps to multiple graphs and resulted in concurrent request to reverse complementing
• added in a few specific GC calls when GROOT is compiled for JS - this is used in the WASP branch

v1.1.0

This release has some performance improvements, both for accuracy and runtime.

• better graph indexing:
  • extend graph windows on a traversal if the next window sketch will be identical
  • merge graph windows for different traversals from the same start node if sketches are identical
• better alignment:
  • use multi hash version of ntHash for KHV minhashing
  • improve exact hierarchical alignment process
• better code:
  • swaps some data structures over for better resource usage (some channels replacing constantly changing slices) and reduce the amount of pointers being passed between functions

** by better - these changes improve runtime, memory usage and accuracy reported by my current tests... Let me know if these changes are working out for you!

v1.0.2

Removes the --plotCov option from GROOT report. This is unfortunate but seems to be needed to get GROOT into conda. There was an upstream dependency (gg) which kept failing the conda tests now the GROOT is using Go 1.14

v1.0.1

Major release which ports over dev work from baby-groot and fixes several GROOT issues. Apologies to users for taking so long to get around to this release! Summary:

• LSH ensemble index - allows variable read length via containment search
• Concurrency improvements - drastically reduces memory use and runtime
• Improved tests
• Minor bug fixes (like meaningful catches for empty input files etc)
• ntHash for minhash
• Go mod support
• Improved handling of duplicate graph windows/sketches
• Prepares codebase for EM on weighted graphs
• Improved db distribution mechanism

v0.8.5

This release replaces LSH Ensemble with LSH Forest. The containment search has been removed for now. This is due LSH Ensemble not indexing graph paths correctly with certain parameters, causing miscalls of some subpaths

v0.8.4

Minor fix:

• clean ARG names before saving PNGs using --plotCov. Some databases have ARGs with slashes in the gene name and this was causing a panic when trying to write filenames containing the ARG.

v0.8.3

• fixes minHash bug introduced at last release
• adds minhash package tests
• updates default indexing parameters

v0.8.2

• swaps GOB to MessagePack for storing index
• exposes maxK and numPartitions for LSH Ensemble
• replaces existing hash functions for MinHash with ntHash
• adds some more unit tests
• performance improvements:
  • lower disk space requirements for index
  • faster indexing and aligning

v0.8.1

This release adds in support for variable read lengths, as requested by several users. The main changes:

• replace the lshForest library with a lshIndex library, which contains both basic LSH Forest and LSH Ensemble
• add --containment flag to indexing command, this indexes the graphs with LSH Ensemble instead of LSH Forest, allowing for containment search of reads against the graph windows.
• general code improvements, tests and fixes

v0.7.1

This is a minor release is to fix the bioconda groot recipe.

• An update to the TAR library used by groot has caused an illegal file path error on some systems. This fix changes the groot get command.