--change-log--
1.8.5 Florian Eggenhofer 6. June 2021
* Compatibility with ghc 9
* Testing with github actions
1.8.0 Florian Eggenhofer 3. January 2020
* Construction start from input alignment for Scan and Alien
* Alien is working fully offline, by using offline taxonomy database
* Improved collection of near identical hits
* RNAlien now uses paralellization
* Fixes for speed regression in taxid positive set computation
1.7.1 Florian Eggenhofer 12. September 2019
* Fixed Scan tool global search step
1.7.0 Florian Eggenhofer 29. August 2019
* Added Scan tool
* Changed tracing high similarity candidates
* Fixed regression in parsing input fasta
1.6.0 Florian Eggenhofer 19. June 2019
* Added offline mode for blast calls and sequence retrieval
* Changed to Biobase repository layout
* Added statically linked executables to releases
1.5.0 Florian Eggenhofer 4. March 2019
* Enabled initialization from multi-line fasta
1.4.0 Florian Eggenhofer 9. December 2018
* Switched to Biobase libraries
* RNAlien is now using json based blast requests
1.3.8 Florian Eggenhofer 3. April 2019
* Fix for outdated ca-certificates
1.3.7 Florian Eggenhofer 13. March 2017
* Removed optimization flags that prevent hackage upload
1.3.6 Florian Eggenhofer 5. March 2017
* SelectSequences moved to own repository, removed tool from package
* Clustal result file is now also written without evaluation step
1.3.5 Florian Eggenhofer 5. March 2017
* Added a commandline switch to check setup and network connection, improved tempdir handling
1.3.4 Florian Eggenhofer 2. March 2017
* More changes toward bioconda compatibility, changed compiler optimization flag to -O
1.3.3 Florian Eggenhofer 1. March 2017
* Further changes to stack.yaml
1.3.2 Florian Eggenhofer 8. February 2017
* Minor fix to stack.yaml for bioconda recipe
1.3.1 Florian Eggenhofer 6. February 2017
* Updated version constraints for ClustalParser supporting multi-line consensus secondary structure
1.3.0 Florian Eggenhofer 20. January 2017
* Included bugfix from ViennaRNAparser concerning RNAalifold systemcall
1.2.9 Florian Eggenhofer 8. January 2017
* Dropped dependency on rnazSelectSequences.pl for evaluation step
* Select sequences can now print a similarity matrix
* Internal sequence selection is substantially faster due to text-metrics
1.2.8 Florian Eggenhofer 1. January 2017
* Added a commandline switch to turn switch the evaluation step on and off
1.2.7 Florian Eggenhofer 13. November 2016
* Fixed a bug in inital connection check with HTTPS
1.2.6 Florian Eggenhofer 12. November 2016
* Changed NCBI URL to HTTPS and updated libary constraints
1.2.5 Florian Eggenhofer 26. October 2016
* Updated stack.yaml
1.2.4 Florian Eggenhofer 24. October 2016
* Support for GHC-8.0.1
1.2.3 Florian Eggenhofer 21. October 2016
* Added cmsearch output to BED12 converter for genome browser integration
* Updated dependency versions and version number output
1.2.2 Florian Eggenhofer 1. June 2016
* Fixed a bug building RNAcentral query and improved formatting of
corresponding output
1.2.1 Florian Eggenhofer 30. May 2016
* Added RNAcentralRequest utility
* Fixed a bug in parsing RNAcentral response headers
1.2.0 Florian Eggenhofer 30. May 2016
* Added cmsearchToBED utility
1.1.3 Florian Eggenhofer 25. April 2016
* Fixed wrong description for softmasking commandline switch
* Fixed encoding tabular iteration progress output
1.1.2 Florian Eggenhofer 18. April 2016
* Fixed a bug in passing softmasking to blast
* Performance improvements in query selection
1.1.1 Florian Eggenhofer 23. March 2016
* Added a commandlineswitch for softmasking
* Improved interface with Alienserver
1.1.0 Florian Eggenhofer 11. February 2016
* Update including changes from 1st review
* Cmbuild uses --refine option
* Evaluation now includes RNAcode result, which is a new dependecy
* RNAcentral lookup for found sequences via REST interface during evaluation
* Added a new alternative query selection method that filters for entries max. pairwise identity
* Added softmasking to blastrequests
* Paralog sequences are now included by default
* Installation of RNAlien is now available via stackage
* Fix several bugs including blasthit coverage filter
* RNAlienStatistics can now parse cmsearch results from multiple cm files as for clans
* RNAlienStatistics includes a switch for using bitscore or evalue cutoffs
1.0.0 Florian Eggenhofer 29. October 2015
* Initial version