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ChangeLog
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ChangeLog
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2015-04-12 Camille Scott <camille.scott.w@gmail.com>
* Make use of LAST's parallel-fasta script to
efficiently parallelize both lastal and hmmscan.
* Update installation docs.
2015-03-25 Camille Scott <camille.scott.w@gmail.com>
* Add handling for non-RNA bases in transcriptome stats task (#49)
* Fix broken verbosity argument
* Fix typo breaking blast remap (#51)
* Add better tests for --user-databases (#51)
2015-03-03 Camille Scott <camille.scott.w@gmail.com>
* Unify internal coordinates as 0-based half-open.
* First iteration of refactored parsers, MafParser.
* Switch to using ali_coord for HMMER.
* Fix the TaskError associated with HMMER remapping
once and for all.
2015-02-25 Camille Scott <camille.scott.w@gmail.com>
* Add missing acceptance test data.
* Remove test transeq task, which isn't tested for.
2015-02-17 Camille Scott <camille.scott.w@gmail.com>
* Refactor DependencyHandler to allow adding additional dependencies.
* Add a version check for LAST.
2016-02-01 Camille Scott <camille.scott.w@gmail.com>
* Temporarily fix a coordinate translation error.
2015-12-15 Camille Scott <camille.scott.w@gmail.com>
* Remap hmmscan coordinates with respect to the
original transcripts.
* Update test data.
* Increment version 0.2.3.
2015-12-10 Camille Scott <camille.scott.w@gmail.com>
* Fix error with output directory creation.
2015-12-10 Camille Scott <camille.scott.w@gmail.com>
* Make BUSCO output dir database-specific.
* Add new _init_filenames() method to AnnotateHandler to
better organize class and allow multiple constructors in
the future.
2015-12-10 Camille Scott <camille.scott.w@gmail.com>
* Update requirements to include numexpr.
* Change the names file to the form
<transcriptome>.dammit.names.csv, to keep in line
with the naming convention.
2015-12-09 Camille Scott <camille.scott.w@gmail.com>
* Add a --evalue flag to filter hits.
2015-12-09 Camille Scott <camille.scott.w@gmail.com>
* Add a --name flag for transcript renaming.
2015-12-04 Camille Scott <camille.scott.w@gmail.com>
* Add FASTA annotation output.
2015-12-02 Camille Scott <camille.scott.w@gmail.com>
* Add separate pip, Ubuntu, and Anaconda install instructions
to documentation.
* Fix remaining issues with the README and documenation install
instructions and test on EC2.
2015-12-02 Camille Scott <camille.scott.w@gmail.com>
* Additional fixes to installation documentation.
* Removed unused taxonomy module.
2015-12-02 Camille Scott <camille.scott.w@gmail.com>
* Fix requirements and installation documentation.
2015-11-25 Camille Scott <camille.scott.w@gmail.com>
* Fix bug when running from different directory.
* Fix syntax error in GFF3 merge task.
2015-11-20 Camille Scott <camille.scott.w@gmail.com>
* Add option to use DAMMIT_DB_DIR environment variable.