original file name: FullAnalysis70x75_2.dn.Neandertal.1.0.53

regionsToProcess
{
	region
	{
		name = "Region0";
		location = "1","1","2046","4094";
		type = "analysis";
	}

	region
	{
		name = "Region1";
		location = "2049","1","2046","4094";
		type = "analysis";
	}

	region
	{
		name = "fake";
		location = "466","1416","10","6";
		type = "background";
	}

	analysisSet
	{
		name = "1";
		background = "fake";
		analysis = "Region0";
	}
	analysisSet
	{
		name = "2";
		background = "fake";
		analysis = "Region1";
	}
}
sequencesToSearchFor
{
    sequence = "1","ATGCAGGATAGGGATAGGGGATAGGGGGATAGGCTTAACTCAATTCTTGTGGGTTATCTCTCTGATATTAGCGCTCAATTACCCTCTGACTTTGTTCAGGGTGTTCAGTTAATTCTCCCGTCTAATGCGCTTCCCTGTTTTTATGTTATTCTCTCTGTAAAGGCTGCTATTTTCATGCATGACACGCAACAGGGGATAGGGACACGCACGCAACAGATGGGAAAGGAGATAGGATCCAAGCTTGGCGTAATCATGGTCATAGCTGTTTCCTGTGTG","ATG","TF120LonG";
	sequence = "1","ATGCCGCAAAAACGCAAAACGCAAACGCAACGCACCAGCCTATGCGCCTGGTCTGTACACCGTTCATCTGTCCTCTTTCAAAGTTGGTCAGTTCGGTTCCCTTATGATTGACCGTCGCATGACACGCAACAGGGGATAGGGACACGCACGCAACAGATGGGAAAGGAGATAGGATCCAAGCTTGGCGTAATCATGGTCATAGCTGTTTCCTGTGTG","ATG","TF90LonG";
	sequence = "1","ATGCTACCTCTCCGCGTAGGCGCTCGTTGGTCCAGCAGAGGCGGCCGCCCTTGCGCGAGCAGAATGGCGGTAGGGGGTCTAGCTGCGTCTCGTCCGGGGGCATGACACGCAACAGGGGATAGGGACACGCACGCAACAGATGGGAAAGGAGATAGGATCCAAGCTTGGCGTAATCATGGTCATAGCTGTTTCCTGTGTG","ATG","TF7LonG";
	sequence = "1","ATGCCAAGCGTACGCACGTGGTTGTTAAAGCTTTTTTGAAAGTTAATCTCCTGGTTCACCGTCTGCTCGTATGCGGTTACCAGGTCGGCGGCCGCCACGTGTGCGCGCGCGGGACTAATCCCGGTTCGCGCGTCGGGCATGACACGCAACAGGGGATAGGGACACGCACGCAACAGATGGGAAAGGAGATAGGATCCAAGCTTGGCGTAATCATGGTCATAGCTGTTTCCTGTGTG","ATG","TF2LonG";
	sequence = "1","ATGCATCCTATCCCTATCCCCTATCCCCCTATTCTCTTGAGGAGTCTCAGCCTCTTAATACTTTCATGTTTCAGAATAATAGGTTCCGAAATAGGCAGGGGGCATTAACTGTTTATACGGGCACTGTTACTCAAGGCACTGACCCCGTTAAAACTTGCATGACACGCAACAGGGGATAGGGACACGCACGCAACAGATGGGAAAGGAGATAGGATCCAAGCTTGGCGTAATCATGGTCATAGCTGTTTCCTGTGTG","ATG","TF100LonG";
	sequence = "1","ATGCGCGTTTTTGCGTTTTGCGTTTGCGTTGCGTTATAACCCAACCTAAGCCGGAGGTTAAAAAGGTAGTCTCTCAGACCTATGATTTTGATAAATTCACTATTGACTCTTCTCAGCGTCTTAATCTAAGCTATCGCTATGTTTTCAAGGATTCTAAGGGAAAATTAATTAATAGCGACGATTTACAGAAGCAAGGGCATGACACGCAACAGGGGATAGGGACACGCACGCAACAGATGG","ATG","Tf150MMP7A";
	sequence = "1","ATGCCGCAAAAACGCAAAACGCAAACGCAACGCATACCTCTCCGCGTAGGCGCTCGTTGGTCCAGCAGAGGCGGCCGCCCTTGCGCGAGCAGAATGGCGGTAGGGGGTCTAGCTGCGTCTCGTCCGGGGGCATGACACGCAACAGGGGATAGGGACACGCACGCAACAGATGG","ATG","Tf9MMP7A";
	sequence = "1","ATGCATCCTATCCCTATCCCCTATCCCCCTATTACCTCTCCGCGTAGGCGCTCGTTGGTCCAGCAGAGGCGGCCGCCCTTGCACGAGCAGAATGGCGGTAGGGGGTCTAGCTGCGTCTCGTCCGGGGGCATGACACGCAACAGGGGATAGGGACACGCACGCAACAGATGG","ATG","Tf10MMP7A-Corrected";
	sequence = "1","ATGCAGGATAGGGATAGGGGATAGGGGGATAGTACCTCTCCGCGTAGGCGCTCGTTGGTCCAGCAGAGGCGGCCGCCCTTGCGCGAGCAGAATGGCGGTAGGGGGTCTAGCTGCGTCTCGTCCGGGGGCATGACACGCAACAGGGGATAGGGACACGCACGCAACAGATGG","ATG","Tf12MMP7A";
	sequence = "1","ATGCGCGTTTTTGCGTTTTGCGTTTGCGTTGCGTTACCTCTCCGCGTAGGCGCTCGTTGGTCCAGCAGAGGCGGCCGCCCTTGCGCGAGCAGAATGGCGGTAGGGGGTCTAGCTGCGTCTCGTCCGGGGGCATGACACGCAACAGGGGATAGGGACACGCACGCAACAGATGG","ATG","Tf15MMP7A";
	sequence = "1","TCAG","TCA","TCAG-key";
	sequence = "1","TGAC","TGA","TGAG-key";
    sequence = "2","ATGCAGGATAGGGATAGGGGATAGGGGGATAGGCTTAACTCAATTCTTGTGGGTTATCTCTCTGATATTAGCGCTCAATTACCCTCTGACTTTGTTCAGGGTGTTCAGTTAATTCTCCCGTCTAATGCGCTTCCCTGTTTTTATGTTATTCTCTCTGTAAAGGCTGCTATTTTCATGCATGACACGCAACAGGGGATAGGGACACGCACGCAACAGATGGGAAAGGAGATAGGATCCAAGCTTGGCGTAATCATGGTCATAGCTGTTTCCTGTGTG","ATG","TF120LonG";
	sequence = "2","ATGCCGCAAAAACGCAAAACGCAAACGCAACGCACCAGCCTATGCGCCTGGTCTGTACACCGTTCATCTGTCCTCTTTCAAAGTTGGTCAGTTCGGTTCCCTTATGATTGACCGTCGCATGACACGCAACAGGGGATAGGGACACGCACGCAACAGATGGGAAAGGAGATAGGATCCAAGCTTGGCGTAATCATGGTCATAGCTGTTTCCTGTGTG","ATG","TF90LonG";
	sequence = "2","ATGCTACCTCTCCGCGTAGGCGCTCGTTGGTCCAGCAGAGGCGGCCGCCCTTGCGCGAGCAGAATGGCGGTAGGGGGTCTAGCTGCGTCTCGTCCGGGGGCATGACACGCAACAGGGGATAGGGACACGCACGCAACAGATGGGAAAGGAGATAGGATCCAAGCTTGGCGTAATCATGGTCATAGCTGTTTCCTGTGTG","ATG","TF7LonG";
	sequence = "2","ATGCCAAGCGTACGCACGTGGTTGTTAAAGCTTTTTTGAAAGTTAATCTCCTGGTTCACCGTCTGCTCGTATGCGGTTACCAGGTCGGCGGCCGCCACGTGTGCGCGCGCGGGACTAATCCCGGTTCGCGCGTCGGGCATGACACGCAACAGGGGATAGGGACACGCACGCAACAGATGGGAAAGGAGATAGGATCCAAGCTTGGCGTAATCATGGTCATAGCTGTTTCCTGTGTG","ATG","TF2LonG";
	sequence = "2","ATGCATCCTATCCCTATCCCCTATCCCCCTATTCTCTTGAGGAGTCTCAGCCTCTTAATACTTTCATGTTTCAGAATAATAGGTTCCGAAATAGGCAGGGGGCATTAACTGTTTATACGGGCACTGTTACTCAAGGCACTGACCCCGTTAAAACTTGCATGACACGCAACAGGGGATAGGGACACGCACGCAACAGATGGGAAAGGAGATAGGATCCAAGCTTGGCGTAATCATGGTCATAGCTGTTTCCTGTGTG","ATG","TF100LonG";
	sequence = "2","ATGCGCGTTTTTGCGTTTTGCGTTTGCGTTGCGTTATAACCCAACCTAAGCCGGAGGTTAAAAAGGTAGTCTCTCAGACCTATGATTTTGATAAATTCACTATTGACTCTTCTCAGCGTCTTAATCTAAGCTATCGCTATGTTTTCAAGGATTCTAAGGGAAAATTAATTAATAGCGACGATTTACAGAAGCAAGGGCATGACACGCAACAGGGGATAGGGACACGCACGCAACAGATGG","ATG","Tf150MMP7A";
	sequence = "2","ATGCCGCAAAAACGCAAAACGCAAACGCAACGCATACCTCTCCGCGTAGGCGCTCGTTGGTCCAGCAGAGGCGGCCGCCCTTGCGCGAGCAGAATGGCGGTAGGGGGTCTAGCTGCGTCTCGTCCGGGGGCATGACACGCAACAGGGGATAGGGACACGCACGCAACAGATGG","ATG","Tf9MMP7A";
	sequence = "2","ATGCATCCTATCCCTATCCCCTATCCCCCTATTACCTCTCCGCGTAGGCGCTCGTTGGTCCAGCAGAGGCGGCCGCCCTTGCACGAGCAGAATGGCGGTAGGGGGTCTAGCTGCGTCTCGTCCGGGGGCATGACACGCAACAGGGGATAGGGACACGCACGCAACAGATGG","ATG","Tf10MMP7A-Corrected";
	sequence = "2","ATGCAGGATAGGGATAGGGGATAGGGGGATAGTACCTCTCCGCGTAGGCGCTCGTTGGTCCAGCAGAGGCGGCCGCCCTTGCGCGAGCAGAATGGCGGTAGGGGGTCTAGCTGCGTCTCGTCCGGGGGCATGACACGCAACAGGGGATAGGGACACGCACGCAACAGATGG","ATG","Tf12MMP7A";
	sequence = "2","ATGCGCGTTTTTGCGTTTTGCGTTTGCGTTGCGTTACCTCTCCGCGTAGGCGCTCGTTGGTCCAGCAGAGGCGGCCGCCCTTGCGCGAGCAGAATGGCGGTAGGGGGTCTAGCTGCGTCTCGTCCGGGGGCATGACACGCAACAGGGGATAGGGACACGCACGCAACAGATGG","ATG","Tf15MMP7A";
	sequence = "2","TCAG","TCA","TCAG-key";
	sequence = "2","TGAC","TGA","TGAG-key";
}
yapParms
{
	maxAlignmentScore = "1.0";
	trimReads = "TRUE";
	minFlows = "50";
	doTraining = "TRUE";
	outputMatches = "TRUE";
	keySize = "26";
	excludedKeys = "ATGC";
	excludedRegions = "";
	sequenceFile = "/data/testYap/Adeno5_corrected.4";
}
qFilterParms
{
	sequFlows = "-1";
	minLength = "50";
    doMixedCheck = "TRUE";
    mixedPositivePercent = "70.0";
    doDotCheck = "TRUE";
    dotFlowPercentCutoff = "5.0";
	qualityFilterToUse = "leiFilter";
	alpha = "20";
	hitsCutOff = "35";
	depth = "0.525";
	quThreshold = "0.8";
	threshold0 = "0.55";
	threshold1 = "0.55";
	threshold2 = "0.55";
	threshold3 = "0.55";
	threshold4 = "1.6";
	minBadBand = "0.5";
	maxBadBand = "0.7";
	maxBadPercent = "3.0";
    doValleyFilter = "TRUE";
    vfMinBadBand1 = "0.4";
    vfMaxBadBand1 = "0.6";
    vfMinBadBand2 = "1.4";
    vfMaxBadBand2 = "1.6";
    vfMinBadBand3 = "2.4";
    vfMaxBadBand3 = "2.6";
    vfLastFlowToTest = "50";
    vfBadFlowThreshold = "4";
    vfMaxFailedPercent = "100.0";
}
buildThresholdListParms
{
	minBadBand = "0.3";
	badCenter = "0.5";
	maxBadBand = "0.7";
	flowsToConsiderForBadBand = "17";
	maxBadBandScore = "0.1";
	smoothEachSide = "2";
	trimWellsFromOutput = "FALSE";
}
wellBasedNucleotideDroopCorrectionParms
{
	windowEachSide = "13";
	stepSize = "1";
	startMinSinglet = "0.75";
	startMaxSinglet = "1.25";
	minSingletsPerWindow = "3";
	reSeedThresholds = "TRUE";
	interpolateVacantWindows = "TRUE";
	useAverage = "TRUE";
	yiJuPadEnd = "FALSE";
}
primerDetectionArgs
{
	doPrimerTrimming = "TRUE";
	minPrimerMatchScore = "0.5";
	numKnownPrimers = "0";
	primer0 = "";
	primer1 = "";
	primer2 = "";
	primer3 = "";
	primer4 = "";
	primer5 = "";
	primer6 = "";
	primer7 = "";
	primer8 = "";
	primer9 = "";
}
pipelineControl
{
	selectedPipeline = "TestFragmentRun";
}
intermediateFileHandling
{
	autoCopyToCluster = "TRUE";
	autoTrimAnalysis = "TRUE";
}
baseCallerThreshList
{
	maxMults = "30";
	threshElement0 = "0.6";
	threshElement1 = "1.6";
	threshElement2 = "2.6";
	threshElement3 = "3.6";
	threshElement4 = "4.6";
	threshElement5 = "5.6";
	threshElement6 = "6.6";
	threshElement7 = "7.6";
	threshElement8 = "8.6";
	threshElement9 = "9.6";
	threshElement10 = "10.6";
	threshElement11 = "11.6";
	threshElement12 = "12.6";
	threshElement13 = "13.6";
	threshElement14 = "14.6";
	threshElement15 = "15.6";
	threshElement16 = "16.6";
	threshElement17 = "17.6";
	threshElement18 = "18.6";
	threshElement19 = "19.6";
	threshElement20 = "20.6";
	threshElement21 = "21.6";
	threshElement22 = "22.6";
	threshElement23 = "23.6";
	threshElement24 = "24.6";
	threshElement25 = "25.6";
	threshElement26 = "26.6";
	threshElement27 = "27.6";
	threshElement28 = "28.6";
	threshElement29 = "29.6";
	threshElement30 = "30.6";
}
normalizeRegionsParms
{
	dcOffset = "495";
	minPPISignal = "80";
	doWellBasedInterpolation = "FALSE";
	attenuationCorrectionFactor = "0.0";
}
cafieCorrectionParms
{
	numParTasks = "4";
	useFastCafie2 = "TRUE";
}
buildWellsParms
{
	removeNeighborContributions = "TRUE";
	minEffect = "370.37";
	maxEffect = "370.556";
	blowByFilter = "mask51_3";
}
findWellCentersParms
{
	centerMask = "2";
	inFromEdge = "3";
	pixelAreaPerWell = "9.6";
	percentWellsWithSequence = "100.0";
	trimMisshapen = "FALSE";
	trimCounts = "70.0";
	removeNeighborContributions = "TRUE";
	minEffect = "0.0";
	maxEffect = "1.0";
	blowByFilter = "mask51_3";
	defineRunKey = "TRUE";
	numKeys = "3";
	runKey = "ATG";
	runKey2 = "TCA";
	runKey3 = "TGA";
	numFlowsToCheck = "8";
}
newblerParms
{
	sequenceKey = "TCAG";
	genomeLength = "1000000";
	processType = mapped;
}
buildWellPixelListsParms
{
    pixelsPerWell = "4";
    trimMisshapen = "FALSE";
}