message: replace --haplotype-window with --haplotype-length
  replaced occurrences of --haplotype-window in examples with --haplotype-length, as described in
diff: @@ -409,7 +409,7 @@ As freebayes is haplotype-based, left-alignment is necessary only for the
  determination of candidate polymorphic loci. Once such loci are determined,
  haplotype observations are extracted from reads where:
  -1. putative variants lie within `--haplotype-window` bases of each other
  +1. putative variants lie within `--haplotype-length` bases of each other
  (default 3bp),
  2. the reference sequence has repeats (e.g. microsatellites or STRs are called
  as one haplotype),
  @@ -449,7 +449,7 @@ detection window. We can then use these as "basis alleles" for the observation
  of haplotypes, considering all other putative variants supported by the
  alignment to be sequencing errors:
  - freebayes -f ref.fa --haplotype-window 500 \
  + freebayes -f ref.fa --haplotype-length 500 \
  --haplotype-basis-alleles vars.vcf aln.bam >haps.vcf
  These steps should allow us to read long haplotypes directly from input data
  @@ -459,7 +459,7 @@ The high error rate means that beyond a small window each read will contain a
  completely different literal haplotype. To a point, this property improves our
  signal to noise ratio and can effectively filter out sequencing errors at the
  point of the input filters, but it also decreases the effective observation
  -depth will prevent the generation of any calls if a long `--haplotype-window`
  +depth will prevent the generation of any calls if a long `--haplotype-length`
  is combined with high a sequencing error rate.
  