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Change Log for SPUMONI

  • This log started being maintained at v2.0.0, therefore, there are not specific version labels for previous versions of SPUMONI besides the git commit id.

v2.0.9 - latest

  • Fixed issue in ms_rle_string() constructor when characters are larger than 127

v2.0.8

  • Fixed bug related to SLP creation when the hash value of first w-mer is mod 0
  • Updated remove temporary file flag to control all the grammar files as well (*.R and *.C)

v2.0.7

  • Worked on speeding up construction of sampled document array

v2.0.6

  • Fixed bug in thirdparty compilation for pfp-thresholds

v2.0.5

  • Fixed bug that occurs when providing a filelist with no document numbers
  • Added some coloring to the logging for SPUMONI

v2.0.4

  • Added the --hash-mod option back to be able to adjust PFP settings
  • TODO: need to update error messages to inform user when PFP crashes

v2.0.3

  • Added *index_stats.txt files that record the memory consumption of index components.

v2.0.2

  • Fixed bug where it looks to check path of document array prior to computation
  • Fixed warning messages in spumoni run, when it says it cannot find a specific file, it was not printing the exact path it was checking so it made it confusing.
  • Updated the usage statment for the -r option in run.

v2.0.1

  • Updated warning message for output index prefix, force users to use './' for same directory files
  • Added check after minimizer digestion to catch scenarios where general text are provided as FASTA files, because the resulting file might be empty and lead to errors.
  • Added ability to not add reverse complement to FASTA files if requested.

v2.0.0

  • Allows for the digestion of input sequences into either a sequence of DNA-based minimizers (e.g ACAT) or minimizers that are alphabet characters themselves.
  • Minimizer digestion is used during build and run sub-commands if requested by the user.
  • Classification test is integrated directly into the SPUMONI code by generating a database of null MS to compare to the online query MS.
  • Classification test is changed to simple threshold test over the maximum positive MS and the largest "common" null MS.
  • Default input reference sequences are FASTA, however, there is a general text option that allows for MS/PML with respect to a "binary" file.
  • Small command-line parsing changes like allowing for output prefix to be specified for index.
  • Initially released via this paper (https://www.biorxiv.org/content/10.1101/2022.09.08.506805v1.abstract)

v1.0.0