Fixed a minor bug which disabled the BWT index building mode.

• Minor release fixing building problems in older versions of GCC.
• Removed some unit tests which had conflicts with libsubunit.

• Fixed a bug where sequenced reads were always mapped to the chr1 for some input files.
• Several minor fixes and improvements.

• Alignment score (AS) was not reported correctly, always scoring 0 or 254. Now it reports all the scores correctly.
• Removed unsupported legacy command-line options to avoid confusion.

The 3.1.1 version includes the following changes:

• Minor bugfixes and optimizations on the pipeline.

The 3.1 version features the following changes compared with the previous version:

• Now the methylation context generated when using the --write-mcontext option is stored in both per-context CSV files and in the optional tag fields of the BAM file alignments, following the Bismark naming convention. Check the user manual for more information on the new SAM tags.
• Several bugfixes involving memory leaks and unused memory.
• Minor performance optimizations.

The 3.0 version uses an optimized Burrows-Wheeler Transform and a modified parallel pipeline to improve the performance.