usage: splitReads -G gkpStore -O ovlStore -Ci input.clearFile -Co output.clearFile -o outputPrefix]

  -G gkpStore    path to read store
  -O ovlStore    path to overlap store

  -o name        output prefix, for logging

  -t bgn-end     limit processing to only reads from bgn to end (inclusive)

  -Ci clearFile  path to input clear ranges (NOT SUPPORTED)
  -Co clearFile  path to output clear ranges

  -e erate       ignore overlaps with more than 'erate' percent error

  -minlength l   reads trimmed below this many bases are deleted