breseq v0.32.0

• If a mutation overlaps multiple genes, its effect on each gene is now annotated.
  (Previously only the first gene encountered was annotated.) The relevant Genome Diff
  fields use a semicolon to separate the information about each impacted gene.
• New output of summary information and settings in JSON format in data directory file
  summary.json.
• Corrected case in polymorphism mode where failing consensus mutations could be
  incorrectly predicted if a polymorphism was rejected. More thorough and consistent
  output of rejection information for RA evidence.
• Updates to VCF output.
• Fixed problem reading some FASTQ files (discovered on Nanopore data).
• More granular options to filter predictions on the coverage of reads supporting them.
  For example:
  --polymorphism-minimum-variant-coverage
--polymorphism-minimum-total-coverage
--polymorphism-minimum-variant-coverage-each-strand
--polymorphism-minimum-total-coverage-each-strand
  WARNING: Previous versions of these options have been renamed for consistency.
• New options to customize bowtie2 options used for alignment. (Only intended for expert users!)
  --bowtie2-scoring, --bowtie2-stage1, --bowtie2-stage2, --bowtie2-junction
• Removed extra slash in paths to invoke R scripts.
• Removed split alignment pieces that were completely soft-padded in output BAM file.
• C++11 is now required for compilation. Optimization added to default compiler settings.
• Fixed compatibility issues when compiling with certain versions of GCC.