breseq v0.35.1

• Fixed bug introduced in v0.35.0 that resulted in displaying an error message that
  "Coverage plot could not be generated" instead of the plot on MC evidence pages.
• Added missing input file 'empty.fastq' needed for ./run_tests.sh.
• Added FASTA output option to gdtools COMPARE/ANNOTATE. This will generate a
  multi-FASTA file with a genotype alignment suitable for building phylogenetic
  trees using parsimony methods. The content is equivalent to that of the PHYLIP
  output option, but without the length limitation on the genome names.
• Added --user-version-as-seq-id option to breseq. If present, it will use the full
  VERSION in an input GenBank file (e.g., NC_001416.1) as the sequence ID instead of
  the LOCUS (e.g., NC_001416). You will need to use the converted reference file
  (data/reference.gff) for further breseq and gdtools operations on breseq output
  generated using this option.
• While not generally recommended, using read and reference file names and output paths
  that contain spaces in them should now work.
• Fixed bug in gdtools ANNOTATE that caused it to fail with --preserve-evidence.
• Miscellaneous improvements to other gdtools subcommands.