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Revision history for App-Sandy
0.25 2023-09-19 14:55:24-03:00 America/Sao_Paulo
- Remove version from transcript_id, example:
ENST00006666.9 will become ENST00006666
0.24 2023-07-31 12:53:42-03:00 America/Sao_Paulo
- When running 'sandy transcriptome' save transcript counts
and gene counts into separated files
- Use GNU/GSL RNG and Randist for randlux algorithm
- Update db.sqlite3 with GTEXv8 expression patterns
- Enable persistent storage of sandy db in docker
- Uppercase all FASTA bases
- Apply NNN blacklist filter
0.23 2019-03-10 17:20:19-03:00 America/Sao_Paulo
- Fix database permissions
- Improve README.md and docker/README.md
0.22 2018-12-20 16:18:05-02:00 America/Sao_Paulo
- Change docker repository to the namespace galantelab
- Change genome command option '--structural-variation'
to '--genomic-variation'
0.21 2018-09-18 20:07:39-03:00 America/Sao_Paulo
- Set expression-matrix as optional
- Fix bash/zsh completion installation
- Distinguish count file between genome (coverage)
and transcriptome (abundance)
- Add compression level option
- Set minimum perl version to 5.014
0.20 2018-09-14 01:49:09-03:00 America/Sao_Paulo
- Add .travis.yml
- Fix count file names
- Testing compression level option
0.19 2018-08-10 21:10:27-03:00 America/Sao_Paulo
- Implement structural variation
- Add variation database
- Add bash/zsh completions
0.18 2018-05-06 02:36:33-03:00 America/Sao_Paulo
- Add citation command
0.17 2018-05-05 22:44:51-03:00 America/Sao_Paulo
- Fix bug in fasta_tree and fasta_rtree
- Populate quality and expression databases
- Improve documentation
- Rename project from App-SimulateReads to App-Sandy
0.16 2018-04-16 00:59:15-03:00 America/Sao_Paulo
- Update quality profile database in order to keep it simple
- Turn read-size option settable only when quality-profile="poisson".
Otherwise, if quality-profile comes from database, it will override
the default/user-provided value
0.15 2018-04-15 02:15:43-03:00 America/Sao_Paulo
- Substitute expression-matrix for weight-file
- Add an expression-matrix database to provide vendor
options for the users
- Change main commands to: genome, transcriptome, custom,
quality and expression. The first three manage simulations
and the last two manage databases
0.14 2018-03-29 03:29:43-03:00 America/Sao_Paulo
- Add seed option for reproducible simulations
- Change weighted raffle from 'role' to 'class'
0.13 2018-03-25 20:40:24-03:00 America/Sao_Paulo
- Add save counts
- SeqId is now case sensitive
0.12 2018-03-24 13:38:37-03:00 America/Sao_Paulo
- Add sequence identifier template
0.11 2018-03-23 18:44:59-03:00 America/Sao_Paulo
- Fix bug when weight-file has just one entry and it is equal to "1"
- Split digest command into genome, transcriptome and custom
0.10 2017-12-03 04:27:18-02:00 America/Sao_Paulo
- Add version option
0.09 2017-11-28 23:24:58-02:00 America/Sao_Paulo
- Fix bug concerning perl versions (5.010 and >=5.018) and
experimental::smartmatch warnings
0.08 2017-11-27 22:21:06-02:00 America/Sao_Paulo
- Fix indexed weight file. If an entry does not exist at the indexed
fasta, then it is removed from the weight file hash
0.07 2017-11-27 11:55:16-02:00 America/Sao_Paulo
- App no more dies if an indexed weighted file has not a valid seqid
recorded at a validated indexed fasta
- Add Dockerfile for the project
0.06 2017-10-29 04:28:50-02:00 America/Sao_Paulo
- Corrected My::Types to App::SimulateReads::Types in Base class
- App no more dies if an indexed fasta sequence has not passed the
length constraints. Instead, that sequence are deleted from the hash
0.05 2017-10-02 22:57:50-03:00 America/Sao_Paulo
- Remove Statistics::Basic
- Test::Perl::Critic and Test::UseAllModules were moved to [TestRecommends]
0.04 2017-09-25 19:16:51-03:00 America/Sao_Paulo
- Minimum perl version set to v5.10
0.03 2017-09-17 22:50:47-03:00 America/Sao_Paulo
- Split App::SimulateReads by creating a CLI::App, CLI::Command interface
0.02 2017-09-16 02:18:05-03:00 America/Sao_Paulo
- Fix README.md issue with PodWeaver by using ReadmeAnyFromPod
0.01 2017-09-15 23:03:14-03:00 America/Sao_Paulo
- Initial version