MrBait v1.2.7

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

MrBait v1.2.6

• 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

MrBait v1.2.5

fixed missing MAF param in multithread load functions

MrBait v1.2.4

• Fixed bug where alleles were miscounted in consensAlign
• Changed consensAlign so that IUPAC ambiguities BDHV randomly resolve to diploid genotype
  -- NOTE: If this behavior is undesired, recode B, D, H, and V ambiguities as needed
• Added --consens_maf option to constrain consensus sequence to alleles above some frequency threshold

MrBait v1.2.3

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

MrBait v1.2.2

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

MrBait v1.2.1

• 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

MrBait v1.2.0

• 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

MrBait v1.1.7

• Fixed bug with changed .loci format in ipyrad
• Fixed bugs with deprecated networkx function calls
• added more options for graph conflict resolution
• allow any number of preceding dashed for flags

MrBait v1.1.6

• 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)