0.3.6

Improves the group command:

• Adds the --subset option as per the dedup command (#74)
• Corrects the flatfile output from the dedup command (#72)

0.3.5

The code has been tweaked to improve run-time.
See #69 for a discussion about the changes implemented.

0.3.4

• Corrects the edit distance comparison used to generate the network for the directional method.
• This will only affect results generated using the directional method and --edit-distance-threshold >1

Previously, using the directional method with the option --edit-distance-threshold set to > 1 did not return the expected set of de-duplicated reads. If you have used the directional method with a threshold >1, we recommend updating UMI-tools and re-running dedup.

0.3.3

• Debugs python 3 compatibility issues
• Adds python 3 tests

0.3.2

Minor bump:
Resolves setuptools-based installation issue

0.3.1

Version bump to allow pypi update. No code changes

0.3.0

• Adds the new group command to group PCR duplicates and return the groups in a tagged BAM file and/or flat file format. This was motivated by multiple requests to group PCR duplicated reads for downstream processes, e,g #45, #54. Special thanks to Nils Koelling (@koelling) for testing the group command.
• Adds the --umi-separator option for dedup and group for workflow where umi_tools extract is not used to extract the UMI. This was motivated by #58

v0.2.6

From v0.2.6 onwards the directional-adjacency method is renamed directional

v0.2.5

• Debugs writing out paired end
• Debugs installation

v0.2.3

Debugs pip installation