v2.1.1

• KmerCamel can compute masked superstrings more efficiently directly from simplitigs (new flag -S)
  • If used, leads to ~10x speedup and memory savings on genomes
• KmerCamel now applies the computation-through-simplitigs optimization only in cases where it is estimated to be helpful. This results to speedups on subsampled pan-genomes.

v2.1.0

• Major speedup of global greedy (about 5x faster and 3x memory lighter on genomes)
• KmerCamel🐫 prints progress reports and simple statistics of the computation (number of k-mers, number of simplitigs)

Backwards compatible, but the results may change due to a possibly different way of handling ties.

v2.0.0

New features of KmerCamel:

• Conversion from (r)SPSS to MS
• Outputting (r)SPSS representing the same k-mer set as MS
• Spliting and joining a MS into a mask and superstring
• KmerCamel can output masked superstring maximizing ones in the mask directly upon construction

Algortimic improvements:

• Streaming algorithm is faster, more memory efficient and supports k up to 127

Improvements and changes in CLI:

• Computation of ms and computation of lowerbounds were separated into subcommands for better clarity
• By deafult, reverse complementary k-mer are now treated as equivalent (can be turned off)
• Flags that are no longer relevant were removed
• Some flags were renamed for better clarity

Due to changes in CLI, this introduces breaking changes.

v1.0.2

Fixed an issue with mask optimization for k>15.

v1.0.1

KmerCamel 🐫 gives a warning if mask convention is violated.

v1.0

• Largely memory and speed optimizations
• Support for k-mers up to 127
• Possible optimization of masks
• Universal support for reading .gz files and for reading from stdin

v0.1

Initial experimental implementation of KmerCamel🐫.