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Version 1.3.0, a big refactor and many other improvements
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@samhunter samhunter released this 31 May 23:10
v1.3.0-release
49a8b67

Changes Include:

  • A major refactor by @joe-angell to make the code cleaner and reduce repetition. Maintaining existing apps and contributing new apps to HTStream will now be easier and involve less coding than ever before.

  • GitHub Continuous Integration support added by @joe-angell.

  • Many changes to add new statistics and standardize statistics collection in order to support better reporting by @msettles. These changes almost certainly break compatability with any tools that collected information from the old JSON log files. Please test before updating. These changes are part of ongoing work to add MultiQC support.

  • Code and repository cleanup by @msettles.

  • Appending to log file no longer requires both -L and -A. Just use -A now. @msettles

  • Added a Code of Conduct and guidelines for contributing. @msettles

  • Moved the repository to a new organization and repository to better represent the contributors associated with the project (https://github.com/s4hts/HTStream). @msettles

  • Major modifications to the way that read filtering is done and added a new hts_LengthFilter applicaton by @keithgmitchell. Previously various different tools had length filtering options, making it difficult to compile accurate logging information about the number of reads discarded due to lenth. The new approach is to only allow length filtering in this one app. Note that other apps can still discard reads for other reasons.

  • Fixed a number of small bugs that were discovered as part of a regression testing system added by @joe-angell

  • Refactoring and a modification of how reads are processed and stored to remove dynamic casting. @joe-angell

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