#Example settings file
#
#--------------------------------------------------------------------------
#The following settings you will likely want to change for your application
#--------------------------------------------------------------------------

#The number of bases to add to each side of each exon/coding sequence
#when determining the regions of interest. 
disperse.roiFlank=10

#The number of extra bases on each flank of each ROI to extract.
#This should be at least the same as max length + max flap. 
disperse.targetFlank=1000

#The minimum content of ROI bases required in a fragment 
$minContent=1

#The minimum length of a fragment
$minLength=100

#The maximum length of a fragment,
#and maximum length of the selected region if flap is used.
$maxLength=200

#The maximum flap length, set to 0 if not using flaps
$maxFlap=500

#The number of bases at each end of the selector probe that will hybridize to the fragment    
$endLength=20

#The restriction reaction file
piecemaker.reactionFile=example_reactions.xml

#The base required at the flap cleavage site.
piecemaker.flapCalculator.base=T

#The maximum number of reaction to pick when evaluating combinations
piecemaker.maxReactions=3

#The location of the vector sequence file.
#probemaker.taglibrary.0=0:/path/to/your.file
probemaker.taglibrary.0=0:example_vector.lib


#--------------------------------------------------------
#The following settings you probably don't want to change
#--------------------------------------------------------

#Restriction digestion settings
piecemaker.strands=3
piecemaker.discardEndFragments=true
piecemaker.preFilter=net.genefront.piecemaker.ops.impl.DuringCutFragmentFilter
piecemaker.preFilter.minContent=${minContent}
piecemaker.preFilter.minLength=${minLength}
piecemaker.preFilter.maxLength=${maxLength}
piecemaker.preFilter.maxFlap=${maxFlap}
piecemaker.preFilter.minSNP=${endLength}

#Flap finder settings
piecemaker.flapCalculator=net.genefront.piecemaker.ops.impl.FivePrimeEndoPositionCalculator
piecemaker.flapCalculator.maxFlap=${maxFlap}
piecemaker.flapCalculator.minRange=${minLength}
piecemaker.flapCalculator.maxRange=${maxLength}
piecemaker.flapCalculator.minSNPRange=${endLength}
piecemaker.flapCalculator.mode=0

#Fragment filter settings
piecemaker.fragmentFilter=net.genefront.piecemaker.ops.impl.DefaultFragmentFilter
piecemaker.fragmentFilter.minContent=${minContent}
piecemaker.fragmentFilter.minLength=${minLength}
piecemaker.fragmentFilter.maxLength=${maxLength}
piecemaker.fragmentFilter.maxFlap=${maxFlap}
piecemaker.fragmentFilter.minSNP=${endLength}

#Combination selection settings
piecemaker.combinationSelector=net.genefront.piecemaker.ops.impl.BaseCoverageOverlapCombinationSelector
piecemaker.combinationSelector.overlap=${endLength}

#Subset selection settings
piecemaker.selectionIterations=1
piecemaker.fragmentSubsetSelector=net.genefront.piecemaker.ops.impl.CoverageOverlapSubSetSelector
piecemaker.fragmentSubsetSelector.overlap=${endLength}

#ProbeMaker settings
probemaker.design.MIN_3_PRIME_ARM_LENGTH=${endLength}
probemaker.design.MAX_3_PRIME_ARM_LENGTH=${endLength}
probemaker.design.MIN_5_PRIME_ARM_LENGTH=${endLength}
probemaker.design.MAX_5_PRIME_ARM_LENGTH=${endLength}
probemaker.targetType=org.moltools.apps.probemaker.ext.target.SelectorTarget
probemaker.targetInputFormat=org.moltools.workbench.ext.form.PieceMakerFormat
probemaker.acceptor=org.moltools.apps.probemaker.ext.acc.AllAcceptor
probemaker.selector=org.moltools.apps.probemaker.ext.sel.NoSelector
