Raptor 3.0.1

This patch release fixes compiler warnings.
Supported compilers: GCC 11, 12, 13

Changelog

Release 3.0.0

New data structure: HIBF

The Hierarchical Interleaved Bloom Filter improves on many aspects of the IBF.
It can be built by running raptor layout and using the resulting layout file as input for raptor build.

General changes

• Improved input validation
• search output contains meta information
• raptor build does not accept --size anymore, instead the false-positive rate is given via --fpr and the size is computed internally

See the help pages, or the documentation for information on usage.

Migration from 2.x.x

You can use raptor upgrade to migrate an old index to the newer version.

Release 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).

Release 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).

Release 1.0.1

Bug fixes

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

Release 1.0.0

Initial release.