v1.3.0

hartleys · Nov 1, 2017 · 39cd1fc · 39cd1fc
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diff --git a/QoRTs-vignette.pdf b/QoRTs-vignette.pdf
diff --git a/QoRTs.jar b/QoRTs.jar
diff --git a/QoRTs_1.3.0.tar.gz b/QoRTs_1.3.0.tar.gz
diff --git a/README.md b/README.md
@@ -1,5 +1,5 @@
-# QoRTs v1.2.42
-(Compiled Fri Jun  2 12:23:55 EDT 2017)
+# QoRTs v1.3.0
+(Compiled Fri Oct 20 11:56:37 EDT 2017)
 
 The [QoRTs software package](http://hartleys.github.io/QoRTs/) is a fast, efficient, and portable 
 multifunction toolkit designed to assist in

diff --git a/example-walkthrough.pdf b/example-walkthrough.pdf
diff --git a/src/HartleyUtils/.cache-main b/src/HartleyUtils/.cache-main
diff --git a/src/HartleyUtils/bin/fileConversionUtils/bamToWiggle$$anonfun$genChrom$1.class b/src/HartleyUtils/bin/fileConversionUtils/bamToWiggle$$anonfun$genChrom$1.class
diff --git a/...HartleyUtils/bin/fileConversionUtils/bamToWiggle$$anonfun$getOverlappedPairBlocks$1.class b/...HartleyUtils/bin/fileConversionUtils/bamToWiggle$$anonfun$getOverlappedPairBlocks$1.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/bamToWiggle$$anonfun$getReadBlocks$1.class b/src/HartleyUtils/bin/fileConversionUtils/bamToWiggle$$anonfun$getReadBlocks$1.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/bamToWiggle$$anonfun$run$1.class b/src/HartleyUtils/bin/fileConversionUtils/bamToWiggle$$anonfun$run$1.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/bamToWiggle$$anonfun$runOnFile2$1.class b/src/HartleyUtils/bin/fileConversionUtils/bamToWiggle$$anonfun$runOnFile2$1.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/bamToWiggle$$anonfun$runOnFile2$2.class b/src/HartleyUtils/bin/fileConversionUtils/bamToWiggle$$anonfun$runOnFile2$2.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/bamToWiggle$$anonfun$writeChrom$1.class b/src/HartleyUtils/bin/fileConversionUtils/bamToWiggle$$anonfun$writeChrom$1.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/bamToWiggle$.class b/src/HartleyUtils/bin/fileConversionUtils/bamToWiggle$.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/bamToWiggle$Chrom$$anonfun$countBlocks$1.class b/src/HartleyUtils/bin/fileConversionUtils/bamToWiggle$Chrom$$anonfun$countBlocks$1.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/bamToWiggle$Chrom$$anonfun$countBlocks$2.class b/src/HartleyUtils/bin/fileConversionUtils/bamToWiggle$Chrom$$anonfun$countBlocks$2.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/bamToWiggle$Chrom$.class b/src/HartleyUtils/bin/fileConversionUtils/bamToWiggle$Chrom$.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/bamToWiggle$Chrom.class b/src/HartleyUtils/bin/fileConversionUtils/bamToWiggle$Chrom.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/bamToWiggle$QcBamToWig$$anonfun$writeOutput$5.class b/src/HartleyUtils/bin/fileConversionUtils/bamToWiggle$QcBamToWig$$anonfun$writeOutput$5.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/bamToWiggle$QcBamToWig$$anonfun$writeOutput$6.class b/src/HartleyUtils/bin/fileConversionUtils/bamToWiggle$QcBamToWig$$anonfun$writeOutput$6.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/bamToWiggle$QcBamToWig.class b/src/HartleyUtils/bin/fileConversionUtils/bamToWiggle$QcBamToWig.class
diff --git a/...in/fileConversionUtils/bamToWiggle$QcBamToWigReservoirSample$$anonfun$writeOutput$1.class b/...in/fileConversionUtils/bamToWiggle$QcBamToWigReservoirSample$$anonfun$writeOutput$1.class
diff --git a/...in/fileConversionUtils/bamToWiggle$QcBamToWigReservoirSample$$anonfun$writeOutput$2.class b/...in/fileConversionUtils/bamToWiggle$QcBamToWigReservoirSample$$anonfun$writeOutput$2.class
diff --git a/...in/fileConversionUtils/bamToWiggle$QcBamToWigReservoirSample$$anonfun$writeOutput$3.class b/...in/fileConversionUtils/bamToWiggle$QcBamToWigReservoirSample$$anonfun$writeOutput$3.class
diff --git a/...in/fileConversionUtils/bamToWiggle$QcBamToWigReservoirSample$$anonfun$writeOutput$4.class b/...in/fileConversionUtils/bamToWiggle$QcBamToWigReservoirSample$$anonfun$writeOutput$4.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/bamToWiggle$QcBamToWigReservoirSample.class b/src/HartleyUtils/bin/fileConversionUtils/bamToWiggle$QcBamToWigReservoirSample.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/bamToWiggle$wiggleMaker.class b/src/HartleyUtils/bin/fileConversionUtils/bamToWiggle$wiggleMaker.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/bamToWiggle.class b/src/HartleyUtils/bin/fileConversionUtils/bamToWiggle.class
diff --git a/...n/fileConversionUtils/prepFlatGtfFile$$anonfun$buildGenomicArrayOfSets_Tx_and_Map$1.class b/...n/fileConversionUtils/prepFlatGtfFile$$anonfun$buildGenomicArrayOfSets_Tx_and_Map$1.class
diff --git a/...prepFlatGtfFile$$anonfun$buildSpliceJunctionMap$2$$anonfun$apply$2$$anonfun$apply$3.class b/...prepFlatGtfFile$$anonfun$buildSpliceJunctionMap$2$$anonfun$apply$2$$anonfun$apply$3.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/prepFlatGtfFile$$anonfun$getFlatGtfIterator$2.class b/src/HartleyUtils/bin/fileConversionUtils/prepFlatGtfFile$$anonfun$getFlatGtfIterator$2.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anon$1$$anonfun$calcBufferLimit$1.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anon$1$$anonfun$calcBufferLimit$1.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anon$1.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anon$1.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anon$2.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anon$2.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anon$3.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anon$3.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anon$4.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anon$4.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anon$5.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anon$5.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$1.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$1.class
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diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$15.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$15.class
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diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$18.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$18.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$19.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$19.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$2.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$2.class
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diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$complementSequenceString$1.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$complementSequenceString$1.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$getAminoAcidFromSeq$1.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$getAminoAcidFromSeq$1.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$getSRPairIter_singleEnd$1.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$getSRPairIter_singleEnd$1.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$initSamRecordIterator$1.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$initSamRecordIterator$1.class
diff --git a/...leyUtils/bin/internalUtils/commonSeqUtils$$anonfun$samRecordPairIterator_resorted$1.class b/...leyUtils/bin/internalUtils/commonSeqUtils$$anonfun$samRecordPairIterator_resorted$1.class
diff --git a/...leyUtils/bin/internalUtils/commonSeqUtils$$anonfun$samRecordPairIterator_unsorted$1.class b/...leyUtils/bin/internalUtils/commonSeqUtils$$anonfun$samRecordPairIterator_unsorted$1.class
diff --git a/...eyUtils/bin/internalUtils/commonSeqUtils$$anonfun$samRecordPairIterator_withMulti$1.class b/...eyUtils/bin/internalUtils/commonSeqUtils$$anonfun$samRecordPairIterator_withMulti$1.class
diff --git a/...n/internalUtils/commonSeqUtils$$anonfun$samRecordPairIterator_withMulti_singleEnd$1.class b/...n/internalUtils/commonSeqUtils$$anonfun$samRecordPairIterator_withMulti_singleEnd$1.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$CigOp$.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$CigOp$.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$CigOp.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$CigOp.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$CigarHolder$$anonfun$cigOps$1.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$CigarHolder$$anonfun$cigOps$1.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$CigarHolder$$anonfun$cigOps$2.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$CigarHolder$$anonfun$cigOps$2.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$CigarHolder$.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$CigarHolder$.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$CigarHolder.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$CigarHolder.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$EmptyFastqReader.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$EmptyFastqReader.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$FastqLine$$anonfun$check$1.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$FastqLine$$anonfun$check$1.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$FastqLine$$anonfun$qualVector$1.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$FastqLine$$anonfun$qualVector$1.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$FastqLine$.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$FastqLine$.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$FastqLine.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$FastqLine.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$FastqReader$.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$FastqReader$.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$FastqReader.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$FastqReader.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$GIVOrdering$class.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$GIVOrdering$class.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$GenomicInterval$.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$GenomicInterval$.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$GenomicInterval.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$GenomicInterval.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$PairIteratorWithLimit.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$PairIteratorWithLimit.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$SamFileAttributes$.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$SamFileAttributes$.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$SamFileAttributes.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$SamFileAttributes.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils.class
diff --git a/src/HartleyUtils/bin/internalUtils/genomicAnnoUtils$.class b/src/HartleyUtils/bin/internalUtils/genomicAnnoUtils$.class
diff --git a/src/HartleyUtils/bin/internalUtils/genomicAnnoUtils$EfficientGenomeSeqContainer.class b/src/HartleyUtils/bin/internalUtils/genomicAnnoUtils$EfficientGenomeSeqContainer.class
diff --git a/...ls/bin/internalUtils/genomicAnnoUtils$EfficientGenomeSeqContainer_FAList$$anonfun$5.class b/...ls/bin/internalUtils/genomicAnnoUtils$EfficientGenomeSeqContainer_FAList$$anonfun$5.class
diff --git a/...lUtils/genomicAnnoUtils$EfficientGenomeSeqContainer_FAList$$anonfun$switchToChrom$3.class b/...lUtils/genomicAnnoUtils$EfficientGenomeSeqContainer_FAList$$anonfun$switchToChrom$3.class
diff --git a/src/HartleyUtils/bin/internalUtils/genomicAnnoUtils$EfficientGenomeSeqContainer_FAList.class b/src/HartleyUtils/bin/internalUtils/genomicAnnoUtils$EfficientGenomeSeqContainer_FAList.class
diff --git a/...Utils/bin/internalUtils/genomicAnnoUtils$EfficientGenomeSeqContainer_MFA$$anonfun$1.class b/...Utils/bin/internalUtils/genomicAnnoUtils$EfficientGenomeSeqContainer_MFA$$anonfun$1.class
diff --git a/...Utils/bin/internalUtils/genomicAnnoUtils$EfficientGenomeSeqContainer_MFA$$anonfun$2.class b/...Utils/bin/internalUtils/genomicAnnoUtils$EfficientGenomeSeqContainer_MFA$$anonfun$2.class
diff --git a/...Utils/bin/internalUtils/genomicAnnoUtils$EfficientGenomeSeqContainer_MFA$$anonfun$3.class b/...Utils/bin/internalUtils/genomicAnnoUtils$EfficientGenomeSeqContainer_MFA$$anonfun$3.class
diff --git a/...Utils/bin/internalUtils/genomicAnnoUtils$EfficientGenomeSeqContainer_MFA$$anonfun$4.class b/...Utils/bin/internalUtils/genomicAnnoUtils$EfficientGenomeSeqContainer_MFA$$anonfun$4.class
diff --git a/...rnalUtils/genomicAnnoUtils$EfficientGenomeSeqContainer_MFA$$anonfun$switchToChrom$1.class b/...rnalUtils/genomicAnnoUtils$EfficientGenomeSeqContainer_MFA$$anonfun$switchToChrom$1.class
diff --git a/...rnalUtils/genomicAnnoUtils$EfficientGenomeSeqContainer_MFA$$anonfun$switchToChrom$2.class b/...rnalUtils/genomicAnnoUtils$EfficientGenomeSeqContainer_MFA$$anonfun$switchToChrom$2.class
diff --git a/src/HartleyUtils/bin/internalUtils/genomicAnnoUtils$EfficientGenomeSeqContainer_MFA.class b/src/HartleyUtils/bin/internalUtils/genomicAnnoUtils$EfficientGenomeSeqContainer_MFA.class
diff --git a/...nternalUtils/genomicAnnoUtils$GenomicArrayOfSets$$anonfun$printGenomicArrayToFile$1.class b/...nternalUtils/genomicAnnoUtils$GenomicArrayOfSets$$anonfun$printGenomicArrayToFile$1.class
diff --git a/...nternalUtils/genomicAnnoUtils$GenomicArrayOfSets$$anonfun$printGenomicArrayToFile$2.class b/...nternalUtils/genomicAnnoUtils$GenomicArrayOfSets$$anonfun$printGenomicArrayToFile$2.class
diff --git a/src/HartleyUtils/bin/internalUtils/genomicAnnoUtils$GenomicArrayOfSets$.class b/src/HartleyUtils/bin/internalUtils/genomicAnnoUtils$GenomicArrayOfSets$.class
diff --git a/src/HartleyUtils/bin/internalUtils/genomicAnnoUtils$GenomicArrayOfSets.class b/src/HartleyUtils/bin/internalUtils/genomicAnnoUtils$GenomicArrayOfSets.class
diff --git a/...nalUtils/genomicAnnoUtils$GenomicArrayOfSets_Generic$$anonfun$finalizeStepVectors$1.class b/...nalUtils/genomicAnnoUtils$GenomicArrayOfSets_Generic$$anonfun$finalizeStepVectors$1.class
diff --git a/...ls/genomicAnnoUtils$GenomicArrayOfSets_Generic$$anonfun$getSteps$1$$anonfun$apply$1.class b/...ls/genomicAnnoUtils$GenomicArrayOfSets_Generic$$anonfun$getSteps$1$$anonfun$apply$1.class
diff --git a/...s/bin/internalUtils/genomicAnnoUtils$GenomicArrayOfSets_Generic$$anonfun$getSteps$1.class b/...s/bin/internalUtils/genomicAnnoUtils$GenomicArrayOfSets_Generic$$anonfun$getSteps$1.class
diff --git a/src/HartleyUtils/bin/internalUtils/genomicAnnoUtils$GenomicArrayOfSets_Generic.class b/src/HartleyUtils/bin/internalUtils/genomicAnnoUtils$GenomicArrayOfSets_Generic.class
diff --git a/...alUtils/genomicAnnoUtils$GenomicArrayOfSets_Stranded$$anonfun$finalizeStepVectors$2.class b/...alUtils/genomicAnnoUtils$GenomicArrayOfSets_Stranded$$anonfun$finalizeStepVectors$2.class
diff --git a/...s/genomicAnnoUtils$GenomicArrayOfSets_Stranded$$anonfun$getSteps$2$$anonfun$apply$2.class b/...s/genomicAnnoUtils$GenomicArrayOfSets_Stranded$$anonfun$getSteps$2$$anonfun$apply$2.class
diff --git a/.../bin/internalUtils/genomicAnnoUtils$GenomicArrayOfSets_Stranded$$anonfun$getSteps$2.class b/.../bin/internalUtils/genomicAnnoUtils$GenomicArrayOfSets_Stranded$$anonfun$getSteps$2.class
diff --git a/src/HartleyUtils/bin/internalUtils/genomicAnnoUtils$GenomicArrayOfSets_Stranded.class b/src/HartleyUtils/bin/internalUtils/genomicAnnoUtils$GenomicArrayOfSets_Stranded.class
diff --git a/...Utils/genomicAnnoUtils$GenomicArrayOfSets_Unstranded$$anonfun$finalizeStepVectors$3.class b/...Utils/genomicAnnoUtils$GenomicArrayOfSets_Unstranded$$anonfun$finalizeStepVectors$3.class
diff --git a/...genomicAnnoUtils$GenomicArrayOfSets_Unstranded$$anonfun$getSteps$3$$anonfun$apply$3.class b/...genomicAnnoUtils$GenomicArrayOfSets_Unstranded$$anonfun$getSteps$3$$anonfun$apply$3.class
diff --git a/...in/internalUtils/genomicAnnoUtils$GenomicArrayOfSets_Unstranded$$anonfun$getSteps$3.class b/...in/internalUtils/genomicAnnoUtils$GenomicArrayOfSets_Unstranded$$anonfun$getSteps$3.class
diff --git a/src/HartleyUtils/bin/internalUtils/genomicAnnoUtils$GenomicArrayOfSets_Unstranded.class b/src/HartleyUtils/bin/internalUtils/genomicAnnoUtils$GenomicArrayOfSets_Unstranded.class
diff --git a/src/HartleyUtils/bin/internalUtils/genomicAnnoUtils$GenomicSpliceJunctionSet$.class b/src/HartleyUtils/bin/internalUtils/genomicAnnoUtils$GenomicSpliceJunctionSet$.class
diff --git a/src/HartleyUtils/bin/internalUtils/genomicAnnoUtils$GenomicSpliceJunctionSet.class b/src/HartleyUtils/bin/internalUtils/genomicAnnoUtils$GenomicSpliceJunctionSet.class
diff --git a/src/HartleyUtils/bin/internalUtils/genomicAnnoUtils$GenomicStepVector$$anon$1.class b/src/HartleyUtils/bin/internalUtils/genomicAnnoUtils$GenomicStepVector$$anon$1.class
diff --git a/src/HartleyUtils/bin/internalUtils/genomicAnnoUtils$GenomicStepVector.class b/src/HartleyUtils/bin/internalUtils/genomicAnnoUtils$GenomicStepVector.class
diff --git a/src/HartleyUtils/bin/internalUtils/genomicAnnoUtils$InternalStepVector$$anon$2.class b/src/HartleyUtils/bin/internalUtils/genomicAnnoUtils$InternalStepVector$$anon$2.class
diff --git a/src/HartleyUtils/bin/internalUtils/genomicAnnoUtils$InternalStepVector$$anon$3.class b/src/HartleyUtils/bin/internalUtils/genomicAnnoUtils$InternalStepVector$$anon$3.class
diff --git a/...yUtils/bin/internalUtils/genomicAnnoUtils$InternalStepVector$$anonfun$addInterval$1.class b/...yUtils/bin/internalUtils/genomicAnnoUtils$InternalStepVector$$anonfun$addInterval$1.class
diff --git a/src/HartleyUtils/bin/internalUtils/genomicAnnoUtils$InternalStepVector$.class b/src/HartleyUtils/bin/internalUtils/genomicAnnoUtils$InternalStepVector$.class
diff --git a/src/HartleyUtils/bin/internalUtils/genomicAnnoUtils$InternalStepVector.class b/src/HartleyUtils/bin/internalUtils/genomicAnnoUtils$InternalStepVector.class
diff --git a/src/HartleyUtils/bin/internalUtils/genomicUtils$$anon$1.class b/src/HartleyUtils/bin/internalUtils/genomicUtils$$anon$1.class
diff --git a/src/HartleyUtils/bin/internalUtils/genomicUtils$$anon$2.class b/src/HartleyUtils/bin/internalUtils/genomicUtils$$anon$2.class
diff --git a/src/HartleyUtils/bin/internalUtils/genomicUtils$$anon$3.class b/src/HartleyUtils/bin/internalUtils/genomicUtils$$anon$3.class
diff --git a/src/HartleyUtils/bin/internalUtils/genomicUtils$$anonfun$1.class b/src/HartleyUtils/bin/internalUtils/genomicUtils$$anonfun$1.class
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diff --git a/...tleyUtils/bin/internalUtils/genomicUtils$$anonfun$getAlignedBasePositionsFromRead$2.class b/...tleyUtils/bin/internalUtils/genomicUtils$$anonfun$getAlignedBasePositionsFromRead$2.class
diff --git a/src/HartleyUtils/bin/internalUtils/genomicUtils$$anonfun$mergeGenomicIntervalSets$1.class b/src/HartleyUtils/bin/internalUtils/genomicUtils$$anonfun$mergeGenomicIntervalSets$1.class
diff --git a/src/HartleyUtils/bin/internalUtils/genomicUtils$$anonfun$truncateCigarBlocks$1.class b/src/HartleyUtils/bin/internalUtils/genomicUtils$$anonfun$truncateCigarBlocks$1.class
diff --git a/src/HartleyUtils/bin/internalUtils/genomicUtils$.class b/src/HartleyUtils/bin/internalUtils/genomicUtils$.class
diff --git a/src/HartleyUtils/bin/internalUtils/genomicUtils$CigarBlock$.class b/src/HartleyUtils/bin/internalUtils/genomicUtils$CigarBlock$.class
diff --git a/src/HartleyUtils/bin/internalUtils/genomicUtils$CigarBlock.class b/src/HartleyUtils/bin/internalUtils/genomicUtils$CigarBlock.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcCigarDistribution$$anonfun$1$$anonfun$apply$mcVI$sp$2.class b/src/HartleyUtils/bin/qcUtils/qcCigarDistribution$$anonfun$1$$anonfun$apply$mcVI$sp$2.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcCigarDistribution$$anonfun$1.class b/src/HartleyUtils/bin/qcUtils/qcCigarDistribution$$anonfun$1.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcCigarDistribution$$anonfun$2$$anonfun$apply$mcVI$sp$3.class b/src/HartleyUtils/bin/qcUtils/qcCigarDistribution$$anonfun$2$$anonfun$apply$mcVI$sp$3.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcCigarDistribution$$anonfun$2.class b/src/HartleyUtils/bin/qcUtils/qcCigarDistribution$$anonfun$2.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcCigarDistribution$$anonfun$4.class b/src/HartleyUtils/bin/qcUtils/qcCigarDistribution$$anonfun$4.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcCigarDistribution$$anonfun$5.class b/src/HartleyUtils/bin/qcUtils/qcCigarDistribution$$anonfun$5.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcCigarDistribution$$anonfun$readCigar$1.class b/src/HartleyUtils/bin/qcUtils/qcCigarDistribution$$anonfun$readCigar$1.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcCigarDistribution$$anonfun$readCigar$2$$anonfun$apply$1.class b/src/HartleyUtils/bin/qcUtils/qcCigarDistribution$$anonfun$readCigar$2$$anonfun$apply$1.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcCigarDistribution$$anonfun$readCigar$2.class b/src/HartleyUtils/bin/qcUtils/qcCigarDistribution$$anonfun$readCigar$2.class
diff --git a/...ils/bin/qcUtils/qcCigarDistribution$$anonfun$writeOpLengthDistribution$1$$anonfun$3.class b/...ils/bin/qcUtils/qcCigarDistribution$$anonfun$writeOpLengthDistribution$1$$anonfun$3.class
diff --git a/...n/qcUtils/qcCigarDistribution$$anonfun$writeOpLengthDistribution$1$$anonfun$apply$2.class b/...n/qcUtils/qcCigarDistribution$$anonfun$writeOpLengthDistribution$1$$anonfun$apply$2.class
diff --git a/...n/qcUtils/qcCigarDistribution$$anonfun$writeOpLengthDistribution$1$$anonfun$apply$3.class b/...n/qcUtils/qcCigarDistribution$$anonfun$writeOpLengthDistribution$1$$anonfun$apply$3.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcCigarDistribution$$anonfun$writeOpLengthDistribution$1.class b/src/HartleyUtils/bin/qcUtils/qcCigarDistribution$$anonfun$writeOpLengthDistribution$1.class
diff --git a/...qcCigarDistribution$$anonfun$writePositionOpDistribution$1$$anonfun$apply$mcVI$sp$1.class b/...qcCigarDistribution$$anonfun$writePositionOpDistribution$1$$anonfun$apply$mcVI$sp$1.class
diff --git a/...HartleyUtils/bin/qcUtils/qcCigarDistribution$$anonfun$writePositionOpDistribution$1.class b/...HartleyUtils/bin/qcUtils/qcCigarDistribution$$anonfun$writePositionOpDistribution$1.class
diff --git a/...HartleyUtils/bin/qcUtils/qcCigarDistribution$$anonfun$writePositionOpDistribution$2.class b/...HartleyUtils/bin/qcUtils/qcCigarDistribution$$anonfun$writePositionOpDistribution$2.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcCigarDistribution$.class b/src/HartleyUtils/bin/qcUtils/qcCigarDistribution$.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcCigarDistribution.class b/src/HartleyUtils/bin/qcUtils/qcCigarDistribution.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcCigarMatch$$anonfun$1.class b/src/HartleyUtils/bin/qcUtils/qcCigarMatch$$anonfun$1.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcCigarMatch$$anonfun$2.class b/src/HartleyUtils/bin/qcUtils/qcCigarMatch$$anonfun$2.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcCigarMatch$$anonfun$3$$anonfun$apply$1.class b/src/HartleyUtils/bin/qcUtils/qcCigarMatch$$anonfun$3$$anonfun$apply$1.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcCigarMatch$$anonfun$3.class b/src/HartleyUtils/bin/qcUtils/qcCigarMatch$$anonfun$3.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcCigarMatch$$anonfun$4.class b/src/HartleyUtils/bin/qcUtils/qcCigarMatch$$anonfun$4.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcCigarMatch$$anonfun$5$$anonfun$apply$2.class b/src/HartleyUtils/bin/qcUtils/qcCigarMatch$$anonfun$5$$anonfun$apply$2.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcCigarMatch$$anonfun$5.class b/src/HartleyUtils/bin/qcUtils/qcCigarMatch$$anonfun$5.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcCigarMatch$$anonfun$6.class b/src/HartleyUtils/bin/qcUtils/qcCigarMatch$$anonfun$6.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcCigarMatch$$anonfun$7$$anonfun$apply$3.class b/src/HartleyUtils/bin/qcUtils/qcCigarMatch$$anonfun$7$$anonfun$apply$3.class
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diff --git a/src/HartleyUtils/bin/qcUtils/qcCigarMatch$$anonfun$8.class b/src/HartleyUtils/bin/qcUtils/qcCigarMatch$$anonfun$8.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcCigarMatch$$anonfun$9.class b/src/HartleyUtils/bin/qcUtils/qcCigarMatch$$anonfun$9.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcCigarMatch$$anonfun$addComparison$1.class b/src/HartleyUtils/bin/qcUtils/qcCigarMatch$$anonfun$addComparison$1.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcCigarMatch$$anonfun$compareOverlappingOps$1.class b/src/HartleyUtils/bin/qcUtils/qcCigarMatch$$anonfun$compareOverlappingOps$1.class
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diff --git a/src/HartleyUtils/bin/qcUtils/qcCigarMatch$$anonfun$mergeComparisons$2.class b/src/HartleyUtils/bin/qcUtils/qcCigarMatch$$anonfun$mergeComparisons$2.class
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diff --git a/src/HartleyUtils/bin/qcUtils/qcCigarMatch$$anonfun$mergeComparisons$4.class b/src/HartleyUtils/bin/qcUtils/qcCigarMatch$$anonfun$mergeComparisons$4.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcCigarMatch$.class b/src/HartleyUtils/bin/qcUtils/qcCigarMatch$.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcCigarMatch.class b/src/HartleyUtils/bin/qcUtils/qcCigarMatch.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$1.class b/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$1.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$12.class b/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$12.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$13.class b/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$13.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$14.class b/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$14.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$15.class b/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$15.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$16.class b/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$16.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$17.class b/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$17.class
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diff --git a/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$19.class b/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$19.class
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diff --git a/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$23.class b/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$23.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$24.class b/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$24.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$3.class b/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$3.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$4.class b/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$4.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$5.class b/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$5.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$6$$anonfun$7.class b/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$6$$anonfun$7.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$6$$anonfun$8.class b/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$6$$anonfun$8.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$6.class b/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$6.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$9$$anonfun$10.class b/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$9$$anonfun$10.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$9$$anonfun$11.class b/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$9$$anonfun$11.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$9$$anonfun$apply$3.class b/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$9$$anonfun$apply$3.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$9$$anonfun$apply$4.class b/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$9$$anonfun$apply$4.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$9.class b/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$9.class
diff --git a/...tleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$getExonsFromRead$1$$anonfun$apply$2.class b/...tleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$getExonsFromRead$1$$anonfun$apply$2.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$getExonsFromRead$1.class b/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$getExonsFromRead$1.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$getSpliceJunctionSetFromRead$1.class b/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$getSpliceJunctionSetFromRead$1.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$getSpliceJunctionSetFromRead$2.class b/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$getSpliceJunctionSetFromRead$2.class
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diff --git a/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$writeOutput$1.class b/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$writeOutput$1.class
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diff --git a/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$writeOutput$3.class b/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$writeOutput$3.class
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diff --git a/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$writeOutput$4.class b/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$$anonfun$writeOutput$4.class
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diff --git a/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$.class b/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt$.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt.class b/src/HartleyUtils/bin/qcUtils/qcFeatureComboCt.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$1.class b/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$1.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$10.class b/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$10.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$11.class b/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$11.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$12.class b/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$12.class
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diff --git a/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$14.class b/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$14.class
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diff --git a/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$17$$anonfun$apply$9.class b/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$17$$anonfun$apply$9.class
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diff --git a/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$calculateGeneBodyCoverage$1.class b/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$calculateGeneBodyCoverage$1.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$countDeletions$1.class b/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$countDeletions$1.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$countInsertions$1.class b/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$countInsertions$1.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$debug_writeGeneBodySpans$1.class b/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$debug_writeGeneBodySpans$1.class
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diff --git a/...tleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$featuresNearRead$1$$anonfun$apply$11.class b/...tleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$featuresNearRead$1$$anonfun$apply$11.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$featuresNearRead$1.class b/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$featuresNearRead$1.class
diff --git a/...ts$$anonfun$geneBody_calculateGeneBodyCoverage_summaries$1$$anonfun$apply$mcVI$sp$1.class b/...ts$$anonfun$geneBody_calculateGeneBodyCoverage_summaries$1$$anonfun$apply$mcVI$sp$1.class
diff --git a/...bin/qcUtils/qcGetGeneCounts$$anonfun$geneBody_calculateGeneBodyCoverage_summaries$1.class b/...bin/qcUtils/qcGetGeneCounts$$anonfun$geneBody_calculateGeneBodyCoverage_summaries$1.class
diff --git a/...ts$$anonfun$geneBody_calculateGeneBodyCoverage_summaries$2$$anonfun$apply$mcVI$sp$2.class b/...ts$$anonfun$geneBody_calculateGeneBodyCoverage_summaries$2$$anonfun$apply$mcVI$sp$2.class
diff --git a/...bin/qcUtils/qcGetGeneCounts$$anonfun$geneBody_calculateGeneBodyCoverage_summaries$2.class b/...bin/qcUtils/qcGetGeneCounts$$anonfun$geneBody_calculateGeneBodyCoverage_summaries$2.class
diff --git a/...bin/qcUtils/qcGetGeneCounts$$anonfun$geneBody_calculateGeneBodyCoverage_summaries$3.class b/...bin/qcUtils/qcGetGeneCounts$$anonfun$geneBody_calculateGeneBodyCoverage_summaries$3.class
diff --git a/...bin/qcUtils/qcGetGeneCounts$$anonfun$geneBody_calculateGeneBodyCoverage_summaries$4.class b/...bin/qcUtils/qcGetGeneCounts$$anonfun$geneBody_calculateGeneBodyCoverage_summaries$4.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$geneBody_geneSizeQuartiles$1.class b/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$geneBody_geneSizeQuartiles$1.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$geneBody_intervalBreaks$1.class b/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$geneBody_intervalBreaks$1.class
diff --git a/...HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$geneLengthMap$1$$anonfun$apply$15.class b/...HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$geneLengthMap$1$$anonfun$apply$15.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$geneLengthMap$1.class b/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$geneLengthMap$1.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$getDeletionSetFromRead$1.class b/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$getDeletionSetFromRead$1.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$getDeletionSetFromRead$2.class b/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$getDeletionSetFromRead$2.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$getIndelSetFromRead$1.class b/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$getIndelSetFromRead$1.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$getIndelSetFromRead$2.class b/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$getIndelSetFromRead$2.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$getInsertionSetFromRead$1.class b/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$getInsertionSetFromRead$1.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$getInsertionSetFromRead$2.class b/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$getInsertionSetFromRead$2.class
diff --git a/...yUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$getPairFeaturesNear$1$$anonfun$apply$13.class b/...yUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$getPairFeaturesNear$1$$anonfun$apply$13.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$getPairFeaturesNear$1.class b/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$getPairFeaturesNear$1.class
diff --git a/...rtleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$getReadFeatures$1$$anonfun$apply$14.class b/...rtleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$getReadFeatures$1$$anonfun$apply$14.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$getReadFeatures$1.class b/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$getReadFeatures$1.class
diff --git a/...HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$helper_findReadIntervalCoverage$1.class b/...HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$helper_findReadIntervalCoverage$1.class
diff --git a/...HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$makeGeneBodyCoverageCountArrays$1.class b/...HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$makeGeneBodyCoverageCountArrays$1.class
diff --git a/...cUtils/qcGetGeneCounts$$anonfun$qcUtils$qcGetGeneCounts$$helper_calculateBreakMap$1.class b/...cUtils/qcGetGeneCounts$$anonfun$qcUtils$qcGetGeneCounts$$helper_calculateBreakMap$1.class
diff --git a/.../qcUtils/qcGetGeneCounts$$anonfun$qcUtils$qcGetGeneCounts$$helper_calculateBreaks$1.class b/.../qcUtils/qcGetGeneCounts$$anonfun$qcUtils$qcGetGeneCounts$$helper_calculateBreaks$1.class
diff --git a/...anonfun$qcUtils$qcGetGeneCounts$$helper_findSpanIntervalCoverage$1$$anonfun$apply$3.class b/...anonfun$qcUtils$qcGetGeneCounts$$helper_findSpanIntervalCoverage$1$$anonfun$apply$3.class
diff --git a/...qcGetGeneCounts$$anonfun$qcUtils$qcGetGeneCounts$$helper_findSpanIntervalCoverage$1.class b/...qcGetGeneCounts$$anonfun$qcUtils$qcGetGeneCounts$$helper_findSpanIntervalCoverage$1.class
diff --git a/...qcGetGeneCounts$$anonfun$qcUtils$qcGetGeneCounts$$helper_findSpanIntervalCoverage$2.class b/...qcGetGeneCounts$$anonfun$qcUtils$qcGetGeneCounts$$helper_findSpanIntervalCoverage$2.class
diff --git a/...eyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$readIsNearFeatures$1$$anonfun$apply$12.class b/...eyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$readIsNearFeatures$1$$anonfun$apply$12.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$readIsNearFeatures$1.class b/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$readIsNearFeatures$1.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$runOnReadPair$1.class b/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$runOnReadPair$1.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$runOnReadPair$2.class b/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$runOnReadPair$2.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$runOnReadPair$3.class b/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$runOnReadPair$3.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$runOnReadPair$4.class b/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$runOnReadPair$4.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$runOnReadPair$5.class b/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$runOnReadPair$5.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$runOnReadPair$6.class b/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$runOnReadPair$6.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$writeGeneBodyCoverage_genewise$1.class b/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$writeGeneBodyCoverage_genewise$1.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$writeOutput$1.class b/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$writeOutput$1.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$writeOutput$2.class b/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$writeOutput$2.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$writeOutput$3.class b/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$writeOutput$3.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$writeOutput$4$$anonfun$22.class b/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$writeOutput$4$$anonfun$22.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$writeOutput$4$$anonfun$23.class b/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$writeOutput$4$$anonfun$23.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$writeOutput$4$$anonfun$24.class b/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$writeOutput$4$$anonfun$24.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$writeOutput$4$$anonfun$25.class b/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$writeOutput$4$$anonfun$25.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$writeOutput$4.class b/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$writeOutput$4.class