File List

Here is a list of all documented files with brief descriptions:

Allele.hpp [code]
AlleleAlignment.hpp [code]
AlleleDiffSegment.hpp [code]
BaseUtil.hpp [code]	File containing definition of the BaseUtil class
CalibratedScorer.hpp [code]
Call.hpp [code]
CallDiff.hpp [code]
CallDiffMatchType.hpp [code]
CallDiffResult.hpp [code]
ChromosomeIdField.hpp [code]
Cigar.hpp [code]
CnvDetailStore.hpp [code]
CnvFileVcfSource.hpp [code]
CnvSegmentStore.hpp [code]
Command.hpp [code]	File containing definition of the Command class
CompactDnaSequence.hpp [code]	File containing definitions CompactDnaSequence class
core.hpp [code]	First header included by all source files
Crr2Fasta.hpp [code]
CrrFile.hpp [code]	File containing definitions CrrFile class
CrrFileWriter.hpp [code]	File containing definition of the CrrFileWriter class
DecodeCrr.hpp [code]
DelimitedFile.hpp [code]
DelimitedLineParser.hpp [code]	File containing definitions of DelimitedLineParser and general purpose DelimitedFieldParsers
Dnb.hpp [code]
Evidence2Cache.hpp [code]
Evidence2Sam.hpp [code]
EvidenceCache.hpp [code]
EvidenceReader.hpp [code]
EvidenceSamUtil.hpp [code]
Exception.hpp [code]	File containing Exception class and assertion macros
Fasta2Crr.hpp [code]
Files.hpp [code]	File containing file system service routines
GapsEstimator.hpp [code]
GeneDataStore.hpp [code]
GenericHistogram.hpp [code]
GenomeMetadata.hpp [code]
IndirectComparator.hpp [code]
Join.hpp [code]
Junction.hpp [code]	This file contains definitions of classes used to manipulate junctions and files containing them
Junction2Vcf.hpp [code]
JunctionCmp.hpp [code]
JunctionCompare.hpp [code]	This file contains definitions of classes used to compare sets of junctions
JunctionDiff.hpp [code]
JunctionStat.hpp [code]	This file contains code that collects diferent junction file statistics
JunctionType.hpp [code]
JunctionVcfRecord.hpp [code]
JunctionVcfWriter.hpp [code]	This file contains procedure for writing junctions to vcf file
LaneBatchCache.hpp [code]
LibraryData.hpp [code]
LibraryReader.hpp [code]
ListCrr.hpp [code]
ListVariants.hpp [code]
Locus.hpp [code]
mainpage.hpp [code]	File containing documentation for the doxygen main page
Map2Sam.hpp [code]
Map2SamConverter.hpp [code]
MapSamUtils.hpp [code]
Md5.hpp [code]	File containing Md5 class for computing md5 checksums
MeiFileVcfSource.hpp [code]
MergedMap2Sam.hpp [code]
MergeMap2SamConverter.hpp [code]
MkVcf.hpp [code]
parse.hpp [code]	File containing general purpose functions parsing strings
PhasedAllele.hpp [code]
PhasedHypothesis.hpp [code]
range.hpp [code]	File containing definitions of Location and Range classes
RangeAnnotationStore.hpp [code]
RangeIntersector.hpp [code]
RangeSet.hpp [code]	File containing definitions of RangeSet class
ReferenceSupportReader.hpp [code]
RepeatMaskerStore.hpp [code]
Sam2Reads.hpp [code]
SamOptions.hpp [code]
SamReader.hpp [code]
SamRecord.hpp [code]
SnpDiff.hpp [code]
Streams.hpp [code]	File containing definitions of InputStream, OutputStream, CompressedInputStream, and CompressedOutputStream
StringSet.hpp [code]
Superlocus.hpp [code]
SuperlocusIterator.hpp [code]
TestVariants.hpp [code]
VarFileCombine.hpp [code]
VarFilter.hpp [code]
VariantFileIterator.hpp [code]
VariantFileVcfSource.hpp [code]
VcfRecordSource.hpp [code]