Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog.

Releases

Bug fix: filter_b BLAST options were incorrectly calling target database
Improved functionality: Parallel processing of BED and GFF files

Fixed bug where single-threaded sliding window target discovery hangs
Changed format of --print commands to reflect start/stop coordinates
New functionality: Added BED inputs and --filter_b --filter_r options
Bug fix: Replaced HDF5 files in targetDiscoverySlidingWindow_parallel to deal with numpy/pyTables version incompatibility
Added consens_maf param setting to output

Bug fix where loci are all lost in multithreading version

Bug fix introduced in 1.2.2 to the filter_targets
Fixed bug with blast_i when applied to baits

Bug fix introduced in 1.2.1 to the blast_i filter
Bug fix causing crash when blast filter returned zero hits

New functionality: Added new BLAST option 'blast_a' to remove ambiguous hits (>1 match)
Added hidden options to add secondary BLAST database
Added --max_hits option for BLAST which maps to BLAST param --max_target_seqs
Bug fix for where --filter_b erroneously rejects blast_x and blast_i options

New functionality: Added capacity to run masking on consensus loci
New functionality: Added option to control masking behavior in VSEARCH for rc and pw filters
Bug fix for -r 2 failing to reset baits from previous run
Bug fix for -r 5 failing to reset baits from previous run

Bug fix with changed ipyrad .loci format
Bug fix with deprecated networkx.edges_iter()
Allow arbitrary leading dashes for flags
Added option to skip graph-based conflict resolution
Added option to do graph-based resolution unweighted
Added option to weight by minimizing N's

Bug fix in reporting for bait design
Bug fix in parallel target selection
Added --target_all option
Added option to design x baits per target with n max overlap (-b calc)
Fixed bug in calculating target IDs for output
Added reverse complement filtering of baits (-f rc)

Bug fix for parsing command line options (-v and -c not working properly)
Bug fix for targets not being added when sliding window exceeds locus

Added --vcfALT option (changes behavior for building consensus from VCF)
Fixed bug in VCF parsing when reference is N or gap
Added --print_loc option
Fixed issue where XMFA hidden 'chunk' files were not deleted

Moved docs to mrbait.readthedocs.io
Bugfix with consensus calling when gap/N content high
Bugfix for XMFA reading
XMFA fie chunking and parallel parsing fixed and added
Minor bug fix in argument parsing

Changed numbering of baits and targets in FASTA output
Added now functional --print_tr option
Other minor edits in response to reviewer criticisms

Now installable via conda
Changes to directory structure
Non-compatible with v1.0.0

Functional version, pre-packaging for conda and before benchmarking

Please see the source code for the most up-to-date development version, and see the complete development history for all changes.