message: coverage_to_regions.py should take ref.fa.fai
  Freebayes-parallel's command-line help erroneously says that coverage_to_regions.py should take the ref.fa as input, when it really wants the fasta's index (i.e. ref.fa.fai as in the other examples).  The default command-line help for coverage_to_regions.py reads in part:
  ...   coverage_to_regions.py  fasta_index num_regions >regions.bed ...
diff: @@ -19,7 +19,7 @@ then
  echo "Generate regions that are equal in terms of data content, and thus have lower variance"
  echo "in runtime. This will yield better resource utilization."
  echo
  - echo " bamtools coverage -in aln.bam | coverage_to_regions.py ref.fa 500 >ref.fa.500.regions"
  + echo " bamtools coverage -in aln.bam | coverage_to_regions.py ref.fa.fai 500 >ref.fa.500.regions"
  echo " freebayes-parallel ref.fa.500.regions 36 -f ref.fa aln.bam >out.vcf"
  echo
  exit
  