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Release 2.0.0
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@eseiler eseiler released this 26 Aug 19:01
raptor-v2.0.0
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eseiler Enrico Seiler
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Learn about vigilant mode.
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Learn about vigilant mode.

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).
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