ganon version 2.0.0 (aka ganon2)

[pirovc]

ganon2 is here (v2.0.0)

Changelog:

• ganon classify --multiple-matches em/lca to choose the algorithm to solve reads with multiple-matches. --reassign option was removed, replaced by --multiple-matches em
• the output file with solved reads has now the extension .one (before .lca in ganon classify and .all in ganon reassign)
• ganon classify can now better control the integrated report generated at the end with --report-type --ranks --min-count and --skip-report
• ganon build and build-custom now generate an HIBF by default with --level species by default on ganon build. The boolean --hibf was removed and --filter-type ibf/hibf introduced.
• Updated to SeqAn3.3.0 and raptor v3.0.1 with some performance improvements (GCC >=11 required).
• Bugfixes and improved documentation

[codecov-commenter]

Codecov Report

Attention: 16 lines in your changes are missing coverage. Please review.

Comparison is base (c50223e) 88.98% compared to head (593f1e4) 88.76%. Report is 4 commits behind head on master.

Files	Patch %	Lines
src/ganon/config.py	82.14%	10 Missing :warning:
src/ganon/build_update.py	78.57%	6 Missing :warning:

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Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #271 +/- ## ========================================== - Coverage 88.98% 88.76% -0.23% ========================================== Files 23 23 Lines 3432 3515 +83 ========================================== + Hits 3054 3120 +66 - Misses 378 395 +17 ```

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