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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).