Revision history for App-Sandy

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