# example CloneLen.rc
# #
# annotations may be found in the lines with a leading "#"
# This file regularly works as a CloneLen.rc file (copy and modify it for your
#   needs), but the annotations will be lost after re-writing by ReadWatcher.pl)
# #
# ------------------------------------------------------------------------------
# array of global assembly resources for sampling of empirical clone insert
#   lengths
# The libraries can make use of these global assembly resources by stating
# the data source identifier
DataSource  {
  # #
  # NOTE: the data source identifier is repeated inside the data structure!
  # the source statement "" consist of
  # - an assembly source, here GAP4 database
  # - optional list of contigs
  # - optional contig selectors (options to Gap.pl)
  Chr1  {
    AssemblySource  /gen/links/dicty/gap/Chr1/CHR1.0 -SlcLen=20000
    id  Chr1
  }
  DY3850  {
    AssemblySource  /gen/links/dicty/gap/DY3850/DY3850.0 JAX4a12a03.s1 JAX4a26b03.s1 JAX4a26b04.s1 JAX4a59e11.s1
    id  DY3850
  }
  mtDNA  {
    AssemblySource  /gen/links/dicty/gap/mtDNA/mtDNA.0 JAX4a06b11.s1
    id  mtDNA
  }
}
# ------------------------------------------------------------------------------
# array of clone libraries
library  {
  # virtual library specifier "default" applies to clones that cannot
  #   associated with any explicitly listed clone library
  default  {
    CutoffValid  2000
    GaussParam  {
      mean  1500
      s  1000
    }
    id  default
  }
  # first library entry
  # The library identifier must correspond to
  # NOTE: the library identifier is repeated inside the data structure!
  JAX4a  {
    # cutoff for statistical calculation:
    #   CutoffSelect is typically smaller than CutoffValid in order to avoid
    #   scew of library's mean measure
    CutoffSelect  1500
    # clone insert length shorter than the following cutoff may be trusted
    CutoffValid  2000
    DataSource  ARRAY{
      {
       # reference to global assembly source,
       #   cf $root{DataSource}{$this->{LibEntry}}
       # This way, assembly sources may be shared by several clone libraries
        LibEntry  DY3850
      }
      {
       # explicit assembly source for sampling of empirical clone insert lengths
        AssemblySource  /gen/links/dicty/gap/DY3850/DY3850.0 JAX4a12a03.s1 JAX4a26b03.s1 JAX4a26b04.s1 JAX4a59e11.s1
        id  JAX4a-DY3850
      }
    }
    # Gaussian distribution parameters of observed clone insert lengths,
    #   automatically updated by program call "ReadWatcher.pl -CloneLen ...".
    # Do not edit, here!
    GaussParam  {
      mean  910.7
      median  939
      n  180
      s  201.133905756073
      var  40454.8480446928
    }
    id  JAX4a
  }
  JC1a  {
    CutoffSelect  5500
    CutoffValid  5300
    DataSource  ARRAY{
      {
        LibEntry  mtDNA
      }
      {
        LibEntry  Chr1
      }
    }
    GaussParam  {
      mean  2484.70127795527
      median  2570
      n  626
      s  1056.23400978304
      var  1115630.28342237
    }
    id  JC1a
  }
}
# ------------------------------------------------------------------------------
# "ReadWatcher.pl -CloneLen ..." reports clone libraries in groups
LibraryGroup  ARRAY{
  {
    # clone insert length range to display in the report that's done by
    # "ReadWatcher.pl -CloneLen ..."
    DispRangeLen  ARRAY{
      0
      5500
    }
    id  JAX4
    library  ARRAY{
      JAX4a
      JAX4b
    }
  }
  {
    DispRangeLen  ARRAY{
      0
      5500
    }
    id  JC1
    library  ARRAY{
      JC1a
      JC1b
      JC1c
    }
  }
}
# ------------------------------------------------------------------------------
# color flute used for combined report produced by "ReadWatcher.pl -CloneLen ..."
# edit only if you know what you're doing
ColorFlute  ARRAY{
  #404040
  #B00020
  #A06000
  #009030
  #0060A0
  #9000A0
}
