Version 1.4.0

• Implemented alignment which can take bigger patches into account, see Alphabet in the manual or any of the examples. (#197)
• Implemented a more gradual variant of EnforceUnique now it can take all reads that score at least x * the highest score. (#146)
• Added a column indicating if a read is placed on a CDR position in the CSV output. (#200)
• Fixed many small bugs in the batchfile parsing. (#205)
• Added support for high contrast theme settings when viewing the HTML report.
• Moved to a hybrid local/global alignment which aligns the reads globally while aligning the template locally. (#157)
• Moved the RawDataDirectory to single peaks definitions instead of having a global setting.

Note

• The benchmarks show a mixed result of the mass based alignment, but as the identity is good enough in comparison with the previous results and the mass based alignment shows very promising result when looked at a case by case basis this result is justified. In the future with more tweaking of the parameters the identity could very likely even be better.
• Performance of this new alignment is worse, a run likely will take 3 times longer, which is expected based on the algorithmic complexity of the mass based alignment algorithm.