v1.2.37

hartleys · May 2, 2017 · 0563b93 · 0563b93
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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_1.2.37.tar.gz b/QoRTs_1.2.37.tar.gz
diff --git a/README.md b/README.md
@@ -1,5 +1,5 @@
-# QoRTs v1.2.26
-(Compiled Tue Mar  7 14:22:03 EST 2017)
+# QoRTs v1.2.37
+(Compiled Mon May  1 14:23:33 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/assembleHSU.sh b/src/HartleyUtils/assembleHSU.sh
@@ -16,4 +16,7 @@ then
   sed -i -e "s/^.*REPLACE_THIS_QORTS_VERSION_VARIABLE_WITH_VERSION_NUMBER.*/$QORTS_VERS_LINE/g" ./src/main/scala/runner/runner.scala
 fi
 
+export _JAVA_OPTIONS="-Xmx1000M -Xms500M -XX:ParallelGCThreads=1"
+export MALLOC_ARENA_MAX=1
+
 sbt < sbtAssemblyCommand.txt
diff --git a/src/HartleyUtils/bin/fileConversionUtils/bamToWiggle$.class b/src/HartleyUtils/bin/fileConversionUtils/bamToWiggle$.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/bamToWiggle$QcBamToWig$$anonfun$writeOutput$1.class b/src/HartleyUtils/bin/fileConversionUtils/bamToWiggle$QcBamToWig$$anonfun$writeOutput$1.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/bamToWiggle$QcBamToWig$$anonfun$writeOutput$2.class b/src/HartleyUtils/bin/fileConversionUtils/bamToWiggle$QcBamToWig$$anonfun$writeOutput$2.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/bamToWiggle$QcBamToWig.class b/src/HartleyUtils/bin/fileConversionUtils/bamToWiggle$QcBamToWig.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/bamToWiggle.class b/src/HartleyUtils/bin/fileConversionUtils/bamToWiggle.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/generatePlotsWithR$$anonfun$1.class b/src/HartleyUtils/bin/fileConversionUtils/generatePlotsWithR$$anonfun$1.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/generatePlotsWithR$$anonfun$2.class b/src/HartleyUtils/bin/fileConversionUtils/generatePlotsWithR$$anonfun$2.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/generatePlotsWithR$.class b/src/HartleyUtils/bin/fileConversionUtils/generatePlotsWithR$.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/generatePlotsWithR$genSimplePlots.class b/src/HartleyUtils/bin/fileConversionUtils/generatePlotsWithR$genSimplePlots.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/generatePlotsWithR.class b/src/HartleyUtils/bin/fileConversionUtils/generatePlotsWithR.class
diff --git a/src/HartleyUtils/bin/fileConversionUtils/runFeatureComboCt$$anonfun$runOnSeqFile$3.class b/src/HartleyUtils/bin/fileConversionUtils/runFeatureComboCt$$anonfun$runOnSeqFile$3.class
diff --git a/src/HartleyUtils/bin/internalUtils/Reporter$$anonfun$1.class b/src/HartleyUtils/bin/internalUtils/Reporter$$anonfun$1.class
diff --git a/src/HartleyUtils/bin/internalUtils/Reporter$$anonfun$closeLogs$1.class b/src/HartleyUtils/bin/internalUtils/Reporter$$anonfun$closeLogs$1.class
diff --git a/src/HartleyUtils/bin/internalUtils/Reporter$$anonfun$closeLogs$2.class b/src/HartleyUtils/bin/internalUtils/Reporter$$anonfun$closeLogs$2.class
diff --git a/src/HartleyUtils/bin/internalUtils/Reporter$$anonfun$closeLogs$3.class b/src/HartleyUtils/bin/internalUtils/Reporter$$anonfun$closeLogs$3.class
diff --git a/src/HartleyUtils/bin/internalUtils/Reporter$$anonfun$error$1.class b/src/HartleyUtils/bin/internalUtils/Reporter$$anonfun$error$1.class
diff --git a/src/HartleyUtils/bin/internalUtils/Reporter$$anonfun$error$2.class b/src/HartleyUtils/bin/internalUtils/Reporter$$anonfun$error$2.class
diff --git a/src/HartleyUtils/bin/internalUtils/Reporter$.class b/src/HartleyUtils/bin/internalUtils/Reporter$.class
diff --git a/src/HartleyUtils/bin/internalUtils/Reporter.class b/src/HartleyUtils/bin/internalUtils/Reporter.class
diff --git a/src/HartleyUtils/bin/internalUtils/commandLineUI$CommandLineArgParser.class b/src/HartleyUtils/bin/internalUtils/commandLineUI$CommandLineArgParser.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
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$10.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$10.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$11.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$11.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$12.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$12.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$13.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$13.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$14$$anonfun$apply$3.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$14$$anonfun$apply$3.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$14.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$14.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$15.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$15.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$16.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$16.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$17.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$17.class
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
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$20.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$20.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$21.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$21.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$22.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$22.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$23.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$23.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$24.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$24.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$25.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$25.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$3.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$3.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$4$$anonfun$apply$1.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$4$$anonfun$apply$1.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$4.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$4.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$5.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$5.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$6$$anonfun$apply$2.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$6$$anonfun$apply$2.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$6.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$6.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$7.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$7.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$8.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$8.class
diff --git a/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$9.class b/src/HartleyUtils/bin/internalUtils/commonSeqUtils$$anonfun$9.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/fileUtils$$anon$1.class b/src/HartleyUtils/bin/internalUtils/fileUtils$$anon$1.class
diff --git a/src/HartleyUtils/bin/internalUtils/fileUtils$$anonfun$1.class b/src/HartleyUtils/bin/internalUtils/fileUtils$$anonfun$1.class
diff --git a/src/HartleyUtils/bin/internalUtils/fileUtils$$anonfun$2.class b/src/HartleyUtils/bin/internalUtils/fileUtils$$anonfun$2.class
diff --git a/...s/bin/internalUtils/fileUtils$$anonfun$getLinesSmartUnzipFromSeq$1$$anonfun$apply$2.class b/...s/bin/internalUtils/fileUtils$$anonfun$getLinesSmartUnzipFromSeq$1$$anonfun$apply$2.class
diff --git a/src/HartleyUtils/bin/internalUtils/fileUtils$$anonfun$getLinesSmartUnzipFromSeq$1.class b/src/HartleyUtils/bin/internalUtils/fileUtils$$anonfun$getLinesSmartUnzipFromSeq$1.class
diff --git a/src/HartleyUtils/bin/internalUtils/fileUtils$$anonfun$skipCommentedInitialLines$1.class b/src/HartleyUtils/bin/internalUtils/fileUtils$$anonfun$skipCommentedInitialLines$1.class
diff --git a/src/HartleyUtils/bin/internalUtils/fileUtils$$anonfun$write2Tab$1.class b/src/HartleyUtils/bin/internalUtils/fileUtils$$anonfun$write2Tab$1.class
diff --git a/src/HartleyUtils/bin/internalUtils/fileUtils$$anonfun$write2Tab$2.class b/src/HartleyUtils/bin/internalUtils/fileUtils$$anonfun$write2Tab$2.class
diff --git a/src/HartleyUtils/bin/internalUtils/fileUtils$$anonfun$write3Tab$1.class b/src/HartleyUtils/bin/internalUtils/fileUtils$$anonfun$write3Tab$1.class
diff --git a/src/HartleyUtils/bin/internalUtils/fileUtils$$anonfun$write3Tab$2.class b/src/HartleyUtils/bin/internalUtils/fileUtils$$anonfun$write3Tab$2.class
diff --git a/src/HartleyUtils/bin/internalUtils/fileUtils$.class b/src/HartleyUtils/bin/internalUtils/fileUtils$.class
diff --git a/...eyUtils/bin/internalUtils/fileUtils$DocWriterUtil$$anonfun$close$1$$anonfun$apply$1.class b/...eyUtils/bin/internalUtils/fileUtils$DocWriterUtil$$anonfun$close$1$$anonfun$apply$1.class
diff --git a/src/HartleyUtils/bin/internalUtils/fileUtils$DocWriterUtil$$anonfun$close$1.class b/src/HartleyUtils/bin/internalUtils/fileUtils$DocWriterUtil$$anonfun$close$1.class
diff --git a/src/HartleyUtils/bin/internalUtils/fileUtils$DocWriterUtil.class b/src/HartleyUtils/bin/internalUtils/fileUtils$DocWriterUtil.class
diff --git a/src/HartleyUtils/bin/internalUtils/fileUtils$SummaryWriter.class b/src/HartleyUtils/bin/internalUtils/fileUtils$SummaryWriter.class
diff --git a/src/HartleyUtils/bin/internalUtils/fileUtils.class b/src/HartleyUtils/bin/internalUtils/fileUtils.class
diff --git a/src/HartleyUtils/bin/internalUtils/genomicAnnoUtils$.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$$anonfun$4.class b/...ls/bin/internalUtils/genomicAnnoUtils$EfficientGenomeSeqContainer_FAList$$anonfun$4.class
diff --git a/...lUtils/genomicAnnoUtils$EfficientGenomeSeqContainer_FAList$$anonfun$switchToChrom$5.class b/...lUtils/genomicAnnoUtils$EfficientGenomeSeqContainer_FAList$$anonfun$switchToChrom$5.class
diff --git a/src/HartleyUtils/bin/internalUtils/genomicAnnoUtils$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$3.class
diff --git a/...rnalUtils/genomicAnnoUtils$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$2.class
diff --git a/...rnalUtils/genomicAnnoUtils$EfficientGenomeSeqContainer_MFA$$anonfun$switchToChrom$3.class b/...rnalUtils/genomicAnnoUtils$EfficientGenomeSeqContainer_MFA$$anonfun$switchToChrom$3.class
diff --git a/...rnalUtils/genomicAnnoUtils$EfficientGenomeSeqContainer_MFA$$anonfun$switchToChrom$4.class b/...rnalUtils/genomicAnnoUtils$EfficientGenomeSeqContainer_MFA$$anonfun$switchToChrom$4.class
diff --git a/src/HartleyUtils/bin/internalUtils/genomicAnnoUtils$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
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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
diff --git a/...tleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$13$$anonfun$apply$7$$anonfun$apply$8.class b/...tleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$13$$anonfun$apply$7$$anonfun$apply$8.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$13$$anonfun$apply$7.class b/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$13$$anonfun$apply$7.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$13.class b/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$13.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$14.class b/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$14.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$15$$anonfun$2.class b/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$15$$anonfun$2.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$15.class b/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$15.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$16$$anonfun$apply$2.class b/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$16$$anonfun$apply$2.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$16.class b/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$16.class
diff --git a/...leyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$17$$anonfun$apply$9$$anonfun$apply$10.class b/...leyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$17$$anonfun$apply$9$$anonfun$apply$10.class
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
diff --git a/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$17.class b/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$17.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$18.class b/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$18.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$19.class b/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$19.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$20.class b/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$20.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$21.class b/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$21.class
diff --git a/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$3.class b/src/HartleyUtils/bin/qcUtils/qcGetGeneCounts$$anonfun$3.class