EPA-ng v0.2.0-beta

Interface Related Changes

• changed CLI library from cxxopts to CLI11
• removed the --repeats option, now repeats are linked to whether or not masking is used (no masking = yes repeats)
• removed the -O option to re-optimize the tree branch lengths and model parameters (this should be done upstream, then pass the parameters via --model)

Feature Changes

• can work with amino acid data again
• removed the experimental "pipeline" parallelization mode
• added masking heuristic, enabled by default
• slightly changed the bfast format to accomodate the masking information
• changed default value of accumulated LWR candidate selection heuristic to 0.99999
• added --model argument that takes either a raxml-ng style model descriptor specifying the exact model parameters to be used, or a RAxML_info file (raxml 8.x) from a -f e run
• added pplacers baseball heuristic, for now with static default settings (--strike-box 3.0, --max-strikes 6, --max-pitches 40)
• added explicit --no-heur flag that disables all preplacement heursitics (does not disable the new masking heuristic!)
• added --no-pre-mask flag to disable masking heuristic
• added --split function that takes a reference MSA file and one or more query aligment files, in phylip format, and outputs a fasta file containing only aligned query sequences. Usage: epa-ng --split ref_alignment query_alignments+. (this is a tailored function to prepare papara output for epa-ng) (issue #16)

Performance Changes

• greatly increased parallel efficiency
• added aforementioned masking heuristic that greatly increases overall performance
• many smaller performance improvements

Bugfixes

• fixed non-working --version option (issue #13)
• fixed issues with RNA data (issue #14)
• fixed a segfault that occured when input query sequence volume got too high (issue #9)
• fixed a bug that allowed empty pqueries to sometimes be printed to the jplace

Code Changes you probably don't care about

• updated genesis and libpll/pll-modules to newer commits
• whole bunch of refactoring
• re-write of the jplace output module, supports MPI I/O operations now to do massively parallel writes, asynchronously. Now scales indefinetly with input volume
• separate, and reworked, mid-level placement functions for preplacement and thorough placement. (treating them differently made a big difference performance wise)
• added a layer of separation to the readers to enable better automatic file format detection
• switched MSA_Stream to use genesis instead of pll for reading
• altered behavior of MSA_Stream slighly
• greatly improved performance lwr calculation
• decreased reliance on Work container
• ressurected the Range and call_focused code :spooky: and used it to implement masking