Purged out a variety of unused and depreciated apps from the primary

build file.  These are still in the code base but won't be added as
apps.

build.properties

@@ -1,4 +1,4 @@
-version=9.0.7
+version=9.0.8
 src.dir=Source
 classes.dir=Classes
 orig.doc.dir=Documentation/USeqDocumentation
@@ -11,28 +11,21 @@ release.master.jar.dir=${release.base.dir}/LibraryJars
 release.worker.jar.dir=${release.base.dir}/Apps
 release.doc.dir=${release.base.dir}/Documentation
 class.select=trans,util,edu,meme
-jar.select=util/apps/ABITraceTCPeakCalculator,\
-edu/utah/seq/vcf/AdetexBafVCFParser,\
-edu/utah/seq/analysis/AggregatePlotter,\
+jar.select=edu/utah/seq/analysis/AggregatePlotter,\
 edu/utah/seq/qc/AggregateQCStats,\
 edu/utah/seq/parsers/AlignmentEndTrimmer,\
-edu/expr/Alleler,\
 edu/utah/seq/analysis/ase/AllelicExpressionComparator,\
 edu/utah/seq/analysis/ase/AllelicExpressionDetector,\
 edu/utah/seq/analysis/ase/AllelicExpressionMerger,\
 edu/utah/seq/analysis/ase/AllelicExpressionRNASeqWriter,\
 edu/utah/seq/analysis/AllelicMethylationDetector,\
 edu/utah/seq/analysis/ArupPipelineWrapper,\
 edu/utah/seq/data/BamContextInspector,\
-edu/utah/seq/base/BamIntensityJoiner,\
-edu/utah/seq/base/BamNMerIntensityParser,\
 edu/utah/seq/data/BamHg19ToB37Converter,\
-edu/utah/seq/vcf/sim/BamSurgeonMutator,\
 edu/utah/seq/vcf/sim/BamBlaster,\
 edu/utah/seq/vcf/sim/BamMixer,\
 trans/misc/Bar2Gr,\
 edu/utah/seq/useq/apps/Bar2USeq,\
-edu/utah/seq/base/BaseClassifier,\
 trans/misc/Bed2Bar,\
 edu/utah/seq/parsers/BedStats,\
 util/bio/annotation/Bed2UCSCRefFlat,\
@@ -43,7 +36,6 @@ edu/utah/seq/analysis/BisStat,\
 edu/utah/seq/analysis/BisStatRegionMaker,\
 edu/utah/seq/data/CalculatePerCycleErrorRate,\
 edu/utah/seq/analysis/ChIPSeq,\
-util/bio/wrappers/CHPCAligner,\
 edu/utah/seq/vcf/cluster/ClusterMultiSampleVCF,\
 edu/utah/seq/parsers/CollectBamStats,\
 util/apps/CompareIntersectingRegions,\
@@ -54,19 +46,13 @@ edu/utah/diagnostics/CountChromosomes,\
 util/bio/seq/BisulfiteConvertFastas,\
 edu/utah/seq/barcodes/Consensus,\
 edu/expr/CorrelationMaps,\
-util/bio/seq/ConvertFastaA2G,\
-util/bio/seq/ConvertFastqA2G,\
-util/bio/seq/ConvertFasta2GCBoolean,\
 util/bio/seq/ConvertFasta2GCBarGraph,\
 edu/utah/seq/analysis/DefinedRegionBisSeq,\
 edu/utah/seq/analysis/DefinedRegionDifferentialSeq,\
 edu/utah/seq/analysis/DefinedRegionRNAEditing,\
 edu/utah/seq/analysis/DefinedRegionScanSeqs,\
 edu/utah/diagnostics/DRDSAnnotator,\
 edu/utah/seq/analysis/EnrichedRegionMaker,\
-edu/utah/seq/parsers/ElandMultiParser,\
-edu/utah/seq/parsers/ElandParser,\
-edu/utah/seq/parsers/ElandSequenceParser,\
 edu/utah/seq/parsers/mpileup/EstimateErrorRates,\
 util/bio/annotation/ExportExons,\
 util/bio/annotation/ExportIntergenicRegions,\
@@ -82,7 +68,6 @@ edu/expr/FileCrossFilter,\
 edu/expr/FileMatchJoiner,\
 util/apps/FileJoiner,\
 util/apps/FileSplitter,\
-edu/utah/seq/parsers/FilterDuplicateAlignments,\
 edu/utah/seq/vcf/xml/FoundationVcfComparator,\
 edu/utah/seq/vcf/xml/FoundationXml2Vcf,\
 edu/utah/seq/vcf/GatkRunner,\
@@ -100,7 +85,6 @@ trans/anno/IntersectRegions,\
 edu/expr/KeggPathwayEnrichment,\
 edu/utah/seq/vcf/LofreqVCFParser,\
 edu/utah/seq/vcf/MafParser,\
-util/bio/parsers/MaqSnps2Bed,\
 util/bio/seq/MakeSpliceJunctionFasta,\
 util/bio/seq/MakeTranscriptome,\
 util/bio/seq/MaskExonsInFastaFiles,\
@@ -139,7 +123,6 @@ util/bio/wrappers/Primer3Wrapper,\
 util/apps/PrintSelectColumns,\
 edu/utah/seq/analysis/QCSeqs,\
 edu/utah/seq/query/QueryIndexer,\
-edu/utah/seq/data/Qseq2Fastq,\
 util/apps/RandomizeTextFile,\
 trans/graphics/RankedSetAnalysis,\
 edu/utah/seq/data/ReadCoverage,\
@@ -156,15 +139,12 @@ edu/utah/seq/parsers/SamAlignmentExtractor,\
 edu/utah/seq/data/SamComparator,\
 edu/utah/seq/parsers/SamParser,\
 edu/utah/seq/parsers/SamTranscriptomeParser,\
-edu/utah/seq/parsers/SamFixer,\
 edu/utah/seq/data/SamSplitter,\
 edu/utah/seq/data/SamReadDepthSubSampler,\
 edu/utah/seq/data/SamSVFilter,\
 edu/utah/seq/data/SamSubsampler,\
 edu/utah/seq/vcf/ScalpelVCFParser,\
 edu/utah/seq/analysis/ScanSeqs,\
-util/bio/parsers/ShiftAnnotationPositions,\
-edu/utah/seq/parsers/SoapV1Parser,\
 util/apps/SubtractRegions,\
 util/apps/ScoreChromosomes,\
 trans/roc/ScoreParsedBars,\
@@ -178,7 +158,6 @@ edu/utah/seq/parsers/Tag2Point,\
 edu/utah/seq/useq/apps/Text2USeq,\
 edu/utah/pysano/TomatoFarmer,\
 edu/utah/seq/analysis/tele/Telescriptor,\
-edu/utah/seq/query/TQuery,\
 edu/utah/seq/useq/apps/UCSCBig2USeq,\
 edu/utah/seq/useq/apps/USeq2UCSCBig,\
 edu/utah/seq/useq/apps/USeq2Text,\