Segway 3.0.5

This is a minor bug fix release. There are some small BED track formatting output fixes from the annotate step. Segway has been updated for a Python 3.10 minimum requirement. As a result, some deprecated packages have been replaced.

Segway (and Genomedata) are both available on Bioconda. With Bioconda installed, to install segway run 'conda install segway'. Segway can still be installed through older methods using "pip", see the Quickstart Guide for details.

Here is a full list of changes made since the last announcement here:

Bug Fixes:

• segway: fix inconsistent thickStart values when merging for final BED output
• replace colorbrewer dependency with palettable
• fix pathlib and pkg_resources deprecations

Known Bugs
To see all known bugs head to the issue tracker.

Segway 3.0.4

This is primarily a bug fix related release. We've re-enabled the --recover option to annotation which was accidentally removed during the 3.0 series release. There was a minor bug where virtual evidence was 1 base pair overzealous in selecting virtual evidence for consideration. We do not suspect this a source of any errors. It's highly recommended to upgrade to avoid these bugs in the future.

Segway (and Genomedata) are both available on Bioconda. With Bioconda installed, to install segway run 'conda install segway'. Segway can still be installed through older methods using "pip", see the Quickstart Guide for details.

Here is a full list of changes made since the last announcement here:

Bug Fixes:

• segway: fix selection of too many potential virtual evidence windows by 1bp
• segway: fix --recover option for annotate task

Enhancements:

• segway: add SegRNA documentation

Known Bugs
To see all known bugs head to the issue tracker

Segway 3.0.3

This is primarily a bug fix related release. This release fixes various installation and distribution issues. It's highly recommended to upgrade to avoid these bugs in the future.

Segway (and Genomedata) are both available on Bioconda. With Bioconda installed, to install segway run 'conda install segway'. Segway can still be installed through older methods using "pip", see the Quickstart Guide for details.

Here is a full list of changes made since the last announcement here:

Bug Fixes:

• segway: fixed posterior label output not working with resolutions greater than 1bp
• segway: fixed bug when using virtual evidence with higher resolutions
• segway: enable virtual evidence for posterior tasks

Known Bugs
To see all known bugs head to the issue tracker

Segway 3.0.2

This is primarily a bug fix related release. This release fixes various installation and distribution issues. It's highly recommended to upgrade to avoid these bugs in the future.

Segway (and Genomedata) are both available on Bioconda. With Bioconda installed, to install segway run 'conda install segway'. Segway can still be installed through older methods using "pip", see the Quickstart Guide for details.

Here is a full list of changes made since the last announcement here:

Bug Fixes:

• segway: added readthedocs configuration file
• segway: added conda environment file
• segway: updated GMTK download locations in documentation
• segway: change GMTK to a runtime only dependency

Known Bugs
To see all known bugs head to the issue tracker

Segway 3.0.1

This is primarily a bug fix related release. This release fixes a regression introduced with virtual evidence with the prior strength option. It's highly recommended to upgrade to avoid these bugs in the future.

Segway (and Genomedata) are both available on Bioconda. With Bioconda installed, to install segway run 'conda install segway'. Segway can still be installed through older methods using "pip", see the Quickstart Guide for details.

Here is a full list of changes made since the last announcement here:

Bug Fixes:

• segway: fixed regression with the prior-strength option
• segway: added manifest file for easier installation on older systems with Python

Known Bugs
To see all known bugs head to the issue tracker