Version 0.18.0

Changes

Strobealign has been ported to Rust. The Rust version is at least as fast and accurate as the C++ version. There are currently some regressions due to the port:

• The Rust version cannot saturate more than about 30-35 cores. Please see issue 561.
• Option --index-statistics is not implemented (this will likely not come back unless someone requests it).
• There are no Python bindings. These were used for experimenting with the algorithm, but Rust makes it easier to do these experiments directly in Rust.

If you need one of the above features, use version 0.17.0 for now.

In addition, the following functional changes have been made:

• Options --nams has been removed.
• #550: Introduce “piecewise“ extension alignment for single-end reads. The previous SSW extension can be enabled with --ssw.
• #595: The in-memory representation of the reference sequence now uses two bits per nucleotide, reducing memory usage of the reference to 25% of its previous size. This change does not affect runtime.
• #607: The reference is now stored as a single concatenated string of all contigs. Reference coordinates now use a single 64-bit value. This means that there are no longer any (relevant) limitations on the number and lengths of contigs.
• #539: Add a "noisy" read profile. Use -P noisy on the command line to select it. This is equivalent to -k 16 -s 12 -l 2 -u 2 -m 100. We found these settings to increase accuracy on error-prone reads (at the cost of runtime).
• #596: Fix not properly paired reads getting MAPQ 60 even if there were alternative equally good mapping locations.
• #624: Fix for secondary alignments: Secondary alignments are now output if their score is at least 0.95 times the score of the primary alignment. This "secondary threshold" can now be set with command-line option --st.