Thesis

State of the implementation at the time of handing in my master's thesis.

0.2.0

Release Notes

Description

Many features were added to allow the practical use of floxer. This includes more alignments due to reverse complementing of reads, sam-formatted output files and many robustness improvents.

Feature list

• various robustness improvements around invalid/odd inputs
• add error probability command line option
• improve help page
• sam-formatted file output
• nicer diagnostic output
• multithreading
• reverse complement alignments

Upcoming features

• Performance improvements
• Large indel, structural variant handling
• MAPQ scores

Version 0.1.0

Release notes

Description

First, barely functional version of floxer.
It now prints the desired exact alignment results to the command line (according to its definition of exactness). It works correctly, at least for one simple test.

Upcoming features and improvements

• write output to .sam/.bam files instead of printing
• command line options for real use cases
• robustness improvements for queries of different lengths to allow benchmarking real usecases
• test benchmark to verify the exactness of the tool
• first performance benchmark against minimap to see what we're dealing with