== Trunk ==

 * Changing distance metric to enum in Rabema.
 * Lowering memory usage of rabema_build_gold_standard by not storing whole GSI in memory but dumping directly.
 * GSI can now be written and read from compressed file.
 * A detailed and updated manual is now available.
 * Using new command line parser yields better documentation.
 * WIT is replaced by GSI file format (gold standard intervals).
 * Rabema can handle BAM now as well as SAM.
 * Rabema has been split into two programs `rabema_build_gold_standard` and `rabema_evaluate`.
 * Sort order of SAM files is now checked on the fly and not at the beginning any more.
 * Oracle also works in Rabema 1.1.
 * Major restructuring of the code, removing unused parts, debug comments etc.
 * Reference sequences are now loaded using an FAI index on demand.
   This reduces the memory requirement for reference sequences to storing the longest contig two times (forward and RC).
 * Improved the output of Rabema to look nicer, progress displays are more exact.
 * Adjusting Rabema to use `bam_io` module and stream through the SAM file.
   The only thing to keep resident in memory is a few integers for each read (not alignment) and a mapping of read names to ids.
   This greatly reduces the memory consumption, e.g. from X GB to Y GB on the example from the Rabema homepage.
 * Added `prepare_sam` tool to prepare the updated RazerS 2 output to be used with new Rabema versions.
   The updated fragment store does not output read sequences for secondary alignments.
   However, this requires a global view and the read sequences to be always in memory.
   The tool accepts a SAM file sorted by query name, copies over sequences from primary alignments to secondary alignments (it knows about paired-end reads).

== Release 1.0 ==

Initial realease for the published paper.
