Raptor 3.0.1
A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences
 
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2.0.0

Features

  • The index additionally stores the original file paths, window size, k-mer size, number of parts, and the data layout (#34, #47, #57, #58):
    • --window, --kmer, --parts, and --compressed are no longer supported when running raptor search.
    • Indices built with an older version of raptor cannot be used with version 2.0.0.
    • Old indices can be converted by running raptor upgrade.
  • New output format (#47):
    • Output includes a header (lines starting with '#').
    • The header assigns an integer to each input file, which are then used in the results:
      #0 /dev/shm/test/data/bin1.fa
      #1 /dev/shm/test/data/bin2.fa
      #2 /dev/shm/test/data/bin3.fa
      #3 /dev/shm/test/data/bin4.fa
      #QUERY_NAME USER_BINS
      query1 0
      query2 0,1
      query3 2,3
    • The list of bins does no longer contain a trailing comma (the last line would have looked like this before 2.0.0: query3 2,3,).
  • Added support for some parts of the SOCKS Interface (#35).

Misc

  • Passing a list of bins is no longer supported. Use a file containing paths to the files instead (#35).

Bug fixes

Except the last entry in this list, these bugs are expected to not be present in version 1.1.0.

  • Validation error when using --compute-minimiser (#25).
  • Typos/Errors in util scripts (#32, #39, #40, #48, #51).
  • Partitioned IBF not working (#50, #53).
  • Rare segmentation fault in threshold computation (#54).

1.1.0

Features

  • Raptor accepts a text file containing the path to a bin on each line (#16).

Bug fixes

  • Threshold option not working (#14).

1.0.1

Bug fixes

  • Reduced the number of open file handles (#10).