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).