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Alphabet.cpp
Alphabet.h
BWT4Codec.h
BWTCodec.h
BitChar.cpp
BitChar.h
BitVector.cpp
BitVector.h
ClusterReader.cpp
ClusterReader.h
Contig.cpp
Contig.h
ContigGraph.cpp
ContigGraph.h
CorrectionThresholds.cpp
CorrectionThresholds.h
DNACodec.h
DNADouble.h
DNAString.cpp
DNAString.h
EncodedString.h
HashMap.h
Interval.cpp
Interval.h
KmerDistribution.cpp
KmerDistribution.h
Makefile.am
Match.cpp
Match.h
Metrics.h
MultiAlignment.cpp
MultiAlignment.h
MultiOverlap.cpp
MultiOverlap.h
NoCodec.h
Pileup.cpp
Pileup.h
PrimerScreen.cpp
PrimerScreen.h
Profiler.h
Quality.cpp
Quality.h
QualityCodec.h
QualityTable.cpp
QualityTable.h
QualityVector.cpp
QualityVector.h
ReadInfoTable.cpp
ReadInfoTable.h
ReadTable.cpp
ReadTable.h
SeqCoord.cpp
SeqCoord.h
SeqDAVG.cpp
SeqDAVG.h
SeqReader.cpp
SeqReader.h
SeqTrie.cpp
SeqTrie.h
SimpleAllocator.h
SimplePool.h
Stats.cpp
Stats.h
StdAlnTools.cpp
StdAlnTools.h
Timer.h
Util.cpp
Util.h
VCFUtil.cpp
VCFUtil.h
bucketSort.cpp
bucketSort.h
mkqs.h
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