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Changelog

v1.0

Results

Compared with v0.2, results have changed in some cases.
Various bugs have been fixed that slighty affected results, improving the results.
Alignment is now performed with a band by default; in rare cases this might degrade results. This may be changed/deactivated via the --band option.

Performance

Significant performance improvements; speed-ups of 3x to more than 10x (depends on data and options).
To achieve full speed, you need to build with machine-specific optimisations (see build instructions).

Features

Dynamically adapt the window size to the length of the current read (via --dyn-w-size).
Automatically cache all input files in a local folder to reduce load on remote ressources (via --cache-data-in-tmp).

Command-line interface

The option --bam2 has been removed; instead just give a list of the combined files as single argument.
The options that influence scoring in alignment have been deprecated. They are no longer visible on the command-line and will be removed in a future update.
Please change all scripts to use the long form of the options (those that begin with --), because a future update will remove/change the short-forms.
The option --dyn-w-size was added (see above).
The option --cache-data-in-tmp was added (see above).

Under-the-hood

Extensive refactoring, modernisation and clean-up of code.
Continuous Integration via Github Actions.
Code-formatting via clang-format.