Version 0.3.0

0.3.0

• Note: The indices produced by previous versions are not guaranteed to be
  compatible unless you used a multi-fasta file. There was a serious
  implementation problem with how bison_index worked when given multiple
  files as input and how multiple files were read into memory in previous
  versions. If you used a multi-fasta file, then everything will continue
  to work correctly. However, if you used multiple fasta files in a list
  then I strongly encourage you to delete the previous indices (just remove
  the bisulfite_genome directory) and reindex. The technical reasons for this
  issue are that when the bison tools previously read multiple fasta files
  into memory, they would do so in whatever order they appeared in the
  directory structure, which can change over time and isn't guaranteed to
  match the order of files someone specified during indexing. While the
  alignments wouldn't be affected by this, the methylation calls could have
  been seriously compromised. In this version, bison_index will only accept a
  directory, not a list of files, and it will always alphasort() the list of
  files in that directory prior to processing. This should eliminate this
  problem. My apologies to anyone affected by this.
• Added --genome-size option to a number of the tools. Many of the bison
  programs need to read the genome into memory. By default, 3 gigabases worth
  of memory are allocated for that and the size increased as needed. For
  smaller genomes, this wasted space. For larger genomes, the constant
  reallocation of space could seriously slow things down. Consequently, this
  option was added to any tool that reads the genome into memory. It's
  convenient to overestimate this slightly, so if your genome is 3.8
  gigabases, then just use 4000000000 as the genome size.
• bison_merge_CpGs can now take multiple input files at once.
• A number of small bug fixes, such as when "genome_dir" doesn't end in a /.