https://github.com/cancerit/hairpin2 - 3.0.0-alpha

Full Changelog: https://github.com/cancerit/hairpin2/compare/2.0.0...3.0.0-alpha

- Python
Published by blex-max 10 months ago

https://github.com/cancerit/hairpin2 - 2.0.0 - DVF filter and improved UI

Introducing the DVF flag, to flag variants which arise from duplicated reads with PCR stutter. In addition to being independently useful, the DVF flag tackles a relatively rare issue users have experienced where internal dupmarking of supporting reads for a given variant left insufficient remaining reads to test ADF and ALF, allowing spurious variants to escape unflagged. These variants would now be flagged DVF. Note that this is not the only use of the DVF flag, as variants may be flagged DVF regardless of the result of their tests for other flags. See the README for info on relevant parameters.

This release also introduces some breaking UI changes - namely that the tool now outputs to stdout, and may be redirected to file using standard shell operations (e.g. ">"); that the name mapping flag now takes a JSON file or JSON-formatted string; and that alignment format is now auto-detected so the format flag is no longer needed. See the README for more details on these, and other more minor UI changes.

Full Changelog: https://github.com/cancerit/hairpin2/compare/1.2.0...2.0.0

- Python
Published by blex-max 10 months ago

https://github.com/cancerit/hairpin2 - 2.0.0 - DVF filter and improved UI

Introducing the DVF flag, which indicates if a variant is only supported by reads which hairpin2 estimates to be stutter duplicates, as described in the README. This flag is useful in its own right, and also addresses an issue some users were having where the dupmarking logic which discounts reads for subsequent testing of ADF and ALF lead to insufficient remaining reads for performing those tests. DVF exposes this dupmarking logic as a flag in and of itself, such that those variants in the case described above would be caught by DVF if not ALF/ADF . Note that this is not the only use of the DVF flag since variants arising from stutter duplicates may also legitimately not trigger the ALF or ADF filters. Check the updated README for information on relevant parameters.

This release also contains breaking UI changes - name mapping is now handled via a JSON, to bring it more in line with expected standards, and output is to stdout and can be sent to file via a redirect. There are also other more minor UI changes which should make the tool more user-friendly. See README for more details.

Full Changelog: https://github.com/cancerit/hairpin2/compare/1.2.0...2.0.0

- Python
Published by blex-max 10 months ago

https://github.com/cancerit/hairpin2 - 1.2.0 - sensitivity improvement

Small update to the core algorithm that a) brings a minor sensitivity increase and b) brings the tool in completely in line with the original paper implementation.

- Python
Published by blex-max about 1 year ago

https://github.com/cancerit/hairpin2 - 1.1.0 - better name mapping UI

What's Changed

• Develop by @blex-max in https://github.com/cancerit/hairpin2/pull/5

Full Changelog: https://github.com/cancerit/hairpin2/compare/1.0.0...1.1.0

- Python
Published by blex-max over 1 year ago

https://github.com/cancerit/hairpin2 - Initial Release!

- Python
Published by blex-max over 1 year ago