Difference between revisions of "STAMP version history"
From Bioinformatics Software
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== v2.0.2 ==
== v2.0.2 ==
Revision as of 22:36, 3 June 2015
- resolves _hierarchy_wrap issue.
- Added support for BIOM profiles.
- Updated manual.
- Added group and multi-group heatmaps.
- Improved speed of table updates.
- Bug fix: Multi-group bar plots were incorrectly scaled by 100.
v2.0.0 (release candidate 6)
- STAMP profiles with 'unclassified' taxa are now handled properly.
- Improved handling of degenerate cases where parent categories have no sequences assigned to them.
v2.0.0 (release candidate 5)
- Added compatibility with MG-RAST LCA profiles.
v2.0.0 (release candidate 4)
- Added option to PCA plots to assign each group a unique shape.
- Fixed issue with MG-RAST profiles. These profiles do not form a strict tree as required by STAMP. A strict tree structure is now enforced by modifying category names that appear multiple times.
- Fixed processing of mothur classify.seqs() results that was causing an error for certain reference taxonomies.
- Fixed bug causing PCA plots to generate an error under some circumstances when clicking on points to determine sample IDs
v2.0.0 (release candidate 3)
- Fixed generation of 'two groups' PCA plots along with various OS X related bugs
v2.0.0 (release candidate 2)
- Fixed bug where STAMP fails due to calculating PCA on a singular matrix.
v2.0.0 (release candidate 1)
- Initial official release of STAMP version 2.
- Provides support for the new functional and organism profiles in MG-RAST v3.0.
- Exploratory scatter plots now support histogram summaries of the distribution of features.
- x-axis labels of relevant plots can now be modified to accommodate profiles where feature counts do not originate from sequences.
- Multi-code COGs can now be treated as separate features or a sequence can be assigned to each COG code.
- Fixed issue with OS X installation which caused the data files required for COG annotations to be missing.
- Fixed bug leading to an infinite loop of error messages when trying to generate excessively large plots.
- Fixed bug causing cursor to remain as a "busy" cursor after configuring a plot.
- Any Python generated error is now displayed to the user to aid in debugging file format issues or reporting possible bugs.
- Extra blank lines in profile files are now ignored.
- File menu items now have more descriptive names making their use more transparent.
- Fixed bug causing the command line execution to produce some output messages even when the verbose option was set to 0.
- Open profile dialog now shows both *.spf and *.txt files by default.
- STAMP can now read profile files with Windows, Unix, or MAC style line endings.
- More informative error messages.
- Fixed bug with label ordering being reversed in extended error plots (bug introduced in v1.02)
- Fixed bug resulting in save tables failing (thanks to Mattias de Hollander for bring this to my attention).
- Fixed bug where last directory was not retained when opening or saving files under Windows XP.
- Added warning dialogs when about to plot profiles containing several hundred features.
- Modified code to remove dependency on PyQt4 and matplotlib when running from the command-line.
- Added unit tests (see STAMP_test.py)
- Initial release