FindPeaks 3.2.0

Obviously, I didn't write an article review this morning. Instead, I finished work on an "unstable" Findpeaks 3.2.0 release. It's now been tagged, for anyone who'd like to download the source code and build it for themselves. The documentation has some catching up to do (which I plan to work on for the end of the week.), but the majority of the features are in place and appear to be functional.

I was debating posting the changelog to SEQanswers, but I think I'll hold off until I have a more stable version. In the meantime, I'll just post a summary from the tag commit here. Welcome to the FindPeaks 3.2 series!

(Update: I should also mention two important details. This release includes code contributions and fixes from Timothee Cezard, another developer at the GSC, as well as a code donation (Lander-Waterman FDR algorithm) from Mikhail Bilenky, also at the GSC.)

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Changes since FindPeaks 3.1.9.2

• New FindPeaks Core Module
• Significant reorganization/modularity/OOP of code
• Significant cleanup of code
• ability to read MAQ .map files
• ability to read bed files (both reduced and extended)
• Log_Buffer to provide buffered and logged output to file
• Several bug fixes to reported issues
• better error handling
• better error messages and verbose output
• New coverage based FDR (Thresholding methods) incorporated
• Native mode (mode 3) for MAQ SET/PET or Bed files, or generating wigs
• Conforms to most Enerjy best practice recommendations. (over 2000 code changes.)
• More controlled exits to handle system crashes gracefully.
• better handling of constants
• smoothing can be turned on or off for adaptive fragment size estimation.
• utilities for working with PETs
• FindPeaks can now be used as a simple wig generator
• hundreds more fixes and updates!