Pre-Release 1.9.4 [2018/02/05]

features and usability improvements

• all new single-executable interface with sub-commands (like git); see the LAMBDA → lambda2-guide (#88, #94)
  • the executable is now called lambda2
  • the subcommands mkindexp, mkindexn, searchp and searchn are currently supported
  • the -p/--program parameter has disappeared, instead one chooses via the command between nucleotide and protein search (#96)
  • many options are now auto-detected from the files, including all index-options and the source alphabets (DNA vs AminoAcid) (#6, #60)
  • all short options are now single-letter, some short-options specifiers where removed (#108)
• man-pages are now automatically generated and included in the packages
• generic and optimised binaries are now shipped within the same package and automatically selected
• index generation is now 30% – 50% faster (#112)

bug fixes

• crash on empty query sequences, fix requires seqan >= 2.4.0 (#111)
• crash if output file is placed given in non-existent or non-writable directory (#113)

compatibility

• the command line interface has changed considerably, please see the LAMBDA → lambda2-guide
• the on-disk index format is compatible to 1.9.3
• requires seqan >= 2.3.1; binary packages based on seqan-2.4.0
• compatible with C++17 if used with seqan >= 2.4.0