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CHANGELOG.md

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Change Log

All notable changes to this project will be documented in this file. This project adheres to Semantic Versioning.

[Unreleased]

Added

  • Header to mRNA->parent map files.
  • New AgnIdFilterStream class to support the --idfile flag of the xtractore program.

Fixed

  • Handling of pseudogene-related mRNA features in NCBI-derived GFF3 files.

[0.16.0] - 2016-05-09

Fixed

  • Outer gene in intron gene cases now designated as a ciLocus.
  • ciLoci are now exempt from merging into miLoci.
  • Fixes to how polycistrons and other edge cases are handled.

[0.15.2] - 2016-03-17

Fixed

  • Minor typo in AgnLocus class.
  • Correct reporting of iLocus type.

[0.15.1] - 2016-01-08

Fixed

  • Updated installation instructions.

[0.15.0] - 2016-01-08

Changed

  • Now using a "label" (accession/Name/ID/position) in place of feature IDs in many places.
  • iLocus children and grandchildren counts are now prefixed with child_, so as to prevent warning messages for features with an uppercase first letter (GFF3 attribute keys starting with an uppercase letter are disallowed except for those declared in the specification).
  • Unit tests adjusted to handle GenomeTools 1.5.8's handling of the gff-version pragma (1 space instead of 3).

Fixed

  • Bug in miloci.py that prevented the last miLocus from printing.
  • Better reporting of issues with gene/mRNA interval containment.
  • Make build order deterministic (to facilitate reproducible builds on, i.e., Debian).
  • Implemented Python 3 support for all ancillary Python scripts.
  • A bug with the locus filtering code that distinguished between reference and prediction loci.
  • Improved build and test environment for systems without Cairo installed.

[0.14.1] - 2015-10-02

Fixed

  • Date in ChangeLog

[0.14.0] - 2015-10-02

Added

  • New post-processing steps to iLocus parsing procedures (iLocus "refinement").
  • An option for using coding sequence instead of UTRs as boundary test for gene overlap when computing iLoci.
  • A variety of new iLocus GFF3 attributes related to iLocus accounting (such as for computing genome breakdown).
  • A barrage of new functional tests (and some unit tests) to validate new functionality.
  • Identification of intron genes into separate iLoci during iLocus parsing.

Changed

  • Replaced ParsEval's --png option with a --nopng option, made graphics the default for HTML output mode.
  • iLocus delta extensions are now \delta bp long, even if that means extending into adjacent gene bodies.
  • Protein-coding genes and non-coding genes are no longer placed in the same iLocus even if they overlap.
  • Enabled use of feature accessions rather than IDs for some tools.
  • Replaced the term empty with the more current term iiLocus in a variety of places in the code and documentation.
  • Refactored iLocus functional test code.

Fixed

  • Bug that prevented AEGeAn from building correctly--thanks Sascha!
  • Bug with option parsing and unknown options/flags (only appeared in Linux).

[0.13.0] - 2015-06-15

Added

  • Ability to filter based on feature attribute key/value pairs.
  • Ability to specify arbitrary parent types for mRNA rep stream, and corresponding --locus flag for the pmrna program.
  • The map option for mRNA rep visitor and pmrna.
  • Ability to access ParsEval locus reports by category (perfect match, CDS match, etc).
  • Delta option for ParsEval.

Fixed

  • Simplified and corrected GAEVAL interval merging function.
  • Fixed locus parsing issues resulting from incorrect sorting of input when pseudonodes involved.

[0.12.2] - 2015-03-06

Fixed

  • Documentation issues (installation instructions and C API docs).

[0.12.1] - 2015-03-06

Fixed

  • Change log formatting issues.
  • Correct year in AgnVersion.h.

Removed

  • Faulty Coverity Scan configuration.

[0.12.0] - 2015-03-05

Fixed

  • Fixed CDS phase correction on the reverse strand.
  • Corrected non-deterministic selection of primary isoform when multiple isoforms have the same (maximum) length.
  • In addition to correcting gene features, AgnPseudogeneFixStream also now corrects transcript and exon features as well.
  • Corrected memory leak in pmrna.
  • Implemented the advertised (but missing) set_source functionality in AgnInferCDSVisitor class.

Changed

  • Locations printed by Xtractore (of the form seqid_start-end) now include a strand character if strand is defined.
  • Began using this specification for maintaining a ChangeLog.

Added

  • Python script for merging iLoci.
  • Documentation for GFF3 expectations, both in general and tool-specific terms.
  • Functional tests for primary mRNA selection and pseudogene correction.
  • Node visitor for calculating coverage and GAEVAL integrity scores.
  • New implementation of GAEVAL that calculates coverage and integrity scores for mRNA features.
  • New branch coverity, which leverages Travis to run Coverity Scan static analysis.

Removed

  • Discarded vestigial AgnNodeDeleteVisitor class.