breseq v0.35.2

IMPORTANT: This release has a KNOWN ISSUE. It does not correctly generate HTML output files.

Please update to v 0.35.3 or later!

• Generation of output files is now multithreaded.
• Changed --use-version-as-seq-id option to --genbank-field-for-seq-id to give more control over
  choosing which part of the header is used for the sequence ID. The default is to assign to the
  first existing field with the preference: LOCUS > ACCESSION > VERSION.
• Fixed GenBank parsing to be more forgiving of different LOCUS lines output by other programs.
  Now only gives a warning if the sequence length is missing and looks for the linear|circular
  designation at different locations within the LOCUS line. Falls back to the source feature
  length if the sequence length is missing from the LOCUS line.
• Changed priority of name used for features in GenBank files to name > gene > locus_tag > label > note.
• Added mutation type INT for applying GenomeDiffs to insert a sequence with annotations.
• Fixed multiple identical GD entry error related to --user-evidence leading to
  double mutation predictions.
• Changed error from loading reference genome files with repeat regions annotated
  with complex/multiple locations to a more informative warning.
• Fixed major memory leak during the output step related to assigning read counts to
  JC evidence from BAM files. Rewrote to further improve performance by making access
  to the required files for this step persistent.
• Added summary.json and output.vcf to the output directory (they are also present in the data directory).
• Fixed --total-only mode for breseq BAM2COV to give expected output in --table mode.