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Updated README.md and WHAT_IS_NEW
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AlignerRefSeqPolicy.h
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BamConverter.h
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BamWriter.h
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Buffer.h
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COPYING
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EBSeq
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EM.cpp
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FOR_CYGWIN_USERS
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GTFItem.h
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Gibbs.cpp
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GroupInfo.h
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HitContainer.h
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HitWrapper.h
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LenDist.h
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Makefile
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Model.h
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ModelParams.h
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NoiseProfile.h
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NoiseQProfile.h
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Orientation.h
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PairedEndHit.h
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PairedEndModel.h
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PairedEndQModel.h
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PairedEndRead.h
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PairedEndReadQ.h
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PolyARules.h
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Profile.h
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QProfile.h
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QualDist.h
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README.md
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RSPD.h
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Read.h
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ReadIndex.h
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ReadReader.h
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RefSeq.h
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RefSeqPolicy.h
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Refs.h
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SamParser.h
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SingleHit.h
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SingleModel.h
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SingleQModel.h
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SingleRead.h
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SingleReadQ.h
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Transcript.h
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Transcripts.h
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WHAT_IS_NEW
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WriteResults.h
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bam2readdepth.cpp
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bam2wig.cpp
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bc_aux.h
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buildReadIndex.cpp
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calcCI.cpp
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convert-sam-for-rsem
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extract-transcript-to-gene-map-from-trinity
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extractRef.cpp
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getUnique.cpp
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model_file_description.txt
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my_assert.h
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parseIt.cpp
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preRef.cpp
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rsem-prepare-reference
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rsem-run-ebseq
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rsem_perl_utils.pm
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samValidator.cpp
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sam_rsem_aux.h
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sam_rsem_cvt.h
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sampling.h
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scanForPairedEndReads.cpp
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simul.h
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simulation.cpp
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synthesisRef.cpp
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tbam2gbam.cpp
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utils.h
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wiggle.cpp
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wiggle.h
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