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# This file contains user-specified targets, i.e. collections of
# executables or directories that are related and are frequently
# rebuilt together.
# Be sure to add any new target to the .PHONY list to prevent any
# silent make problems.
.PHONY: everything all depend clean execs_size nolink dogtools
.PHONY: assembler layoutold augment closure fintools simtools utilities 454tools
all: everything
assembler: assemble assemble_alt layout ueberal tiled assisted reporting qcmarkup
layoutold: layout
utilities: util
simtools: simulation
fintools: finishing
closure: human_closure
augment: augment_aligns
454tools: AddAlignsToFlowInfo CallWithCutoffs DetermineAcceptedReads \
EvaluateUniformity FilterByConsecutive FilterByKey FilterByOverlap \
FastaSizes LoadInfoFile MakeFastaSubset \
MakeLookupTable NormalizeFlows ProximityAnalysis QueryLookupTable \
RemoveShortReads Realign454 RightTrimA SortOutNames SummarizeRegion \
TrimToAlign UpdateFlowInfo Wells2Flowb TrimByBad RightTrimB
solexaPipeline: text ExtractSolexaFasta FeudalSize ParamsByRead SolexaFilters QualsFromSolexa SolexaComputeMetrics SolexaComputePerfectAligns FastaSizes ShortQueryLookup ImperfectLookupTable BestAlignmentTable AlignParamsByRead SelectPassing ProcessChIPData CoverageHistFromAligns ComputeBiasFromIntensities ComputeRegionalSimilarity BiasPiles_Solexa ComputeImageMetrics AverageImageMetrics GetSolexaClusterSize AddSolexaClusterSizeMetric BiasPlotGC_Solexa PairedReadParamsByRead
dogtools: dogMapping
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