v2.0.0

Second Major Version:

1. Updated Rust-Bio data structures.
   • This includes a sampled suffix array which reduces the size of the MG-Indices.
   • Indices built with different major versions will not be compatible.
2. New output format.
   • The binning output now reports the alignment edit distance for hits.
   • The collapse command works with this new output and will not be compatible with previous output format
3. New inputs allowed.
   • The binning command now accepts either FASTA or FASTQ format inputs.
   • The queries no longer need to be the same size.
4. Parameter changes
   • To account for different size queries, the binning parameters have been modified.
   • The edit distance is now a proportion (--edit-rate) based on the length of the read.
   • The --seed-gap parameter was renamed --seed-interval to be more consistent with other tools.
   • The minimum seed threshold (--min-seed) is now a percentage of the number of seeds to allow different size reads.

What's Changed

• Dev by @tfursten in #1
• build FM-index from ssa references by @tfursten in #2
• Dev by @tfursten in #3
• Dev by @tfursten in #4
• Update tests by @tfursten in #5
• update stopwatch by @tfursten in #6

Full Changelog: 1.0.2...2.0.0