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

bam |
examples |
pileup |
Main.cpp |
printRefPositions |
Main.cpp |
PrintRefPositions.cpp |
PrintRefPositions.h |
test |
BamIndexTest.cpp |
BamIndexTest.h |
Main.cpp |
Modify.cpp |
Modify.h |
ModifyVar.cpp |
ModifyVar.h |
ReadFiles.cpp |
ReadFiles.h |
SamFileTest.cpp |
SamFileTest.h |
ShiftIndels.cpp |
ShiftIndels.h |
TestCigarHelper.cpp |
TestCigarHelper.h |
TestEquals.cpp |
TestEquals.h |
TestFilter.cpp |
TestFilter.h |
TestPileup.cpp |
TestPileup.h |
TestPosList.cpp |
TestPosList.h |
TestSamCoordOutput.cpp |
TestSamCoordOutput.h |
TestSamRecordHelper.cpp |
TestSamRecordHelper.h |
TestSamRecordPool.cpp |
TestSamRecordPool.h |
TestValidate.cpp |
TestValidate.h |
ValidationTest.cpp |
ValidationTest.h |
WriteFiles.cpp |
WriteFiles.h |
BamIndex.cpp |
BamIndex.h |
BamInterface.cpp |
BamInterface.h |
CigarHelper.cpp |
CigarHelper.h |
GenericSamInterface.cpp |
GenericSamInterface.h |
Pileup.h |
PileupElement.cpp |
PileupElement.h |
PileupElementBaseQual.cpp |
PileupElementBaseQual.h |
PosList.cpp |
PosList.h |
SamCoordOutput.cpp |
SamCoordOutput.h |
SamFile.cpp |
SamFile.h |
SamFileHeader.cpp |
SamFileHeader.h |
SamFilter.cpp |
SamFilter.h |
SamFlag.h |
SamHeaderHD.cpp |
SamHeaderHD.h |
SamHeaderPG.cpp |
SamHeaderPG.h |
SamHeaderRecord.cpp |
SamHeaderRecord.h |
SamHeaderRG.cpp |
SamHeaderRG.h |
SamHeaderSQ.cpp |
SamHeaderSQ.h |
SamHeaderTag.cpp |
SamHeaderTag.h |
SamHelper.h |
SamInterface.cpp |
SamInterface.h |
SamQuerySeqWithRefHelper.cpp |
SamQuerySeqWithRefHelper.h |
SamRecord.cpp |
SamRecord.h |
SamRecordHelper.cpp |
SamRecordHelper.h |
SamRecordPool.cpp |
SamRecordPool.h |
SamReferenceInfo.cpp |
SamReferenceInfo.h |
SamStatistics.cpp |
SamStatistics.h |
SamStatus.h |
SamTags.cpp |
SamTags.h |
SamValidation.cpp |
SamValidation.h |
fastq |
test |
FastQFileTest.cpp |
BaseComposition.cpp |
BaseComposition.h |
BaseCount.cpp |
BaseCount.h |
FastQFile.cpp |
FastQFile.h |
FastQStatus.cpp |
FastQStatus.h |
general |
test |
baseUtilitiesTest |
BaseUtilitiesTest.cpp |
BaseUtilitiesTest.h |
cigar |
CigarRollerTest.cpp |
CigarRollerTest.h |
dbsnp |
Main.cpp |
inputFileTest |
InputFileTest.cpp |
InputFileTest.h |
memoryMapArrayTest |
MemoryMapArrayTest.cpp |
MemoryMapArrayTest.h |
nonOverlapRegions |
NonOverlapRegionsTest.cpp |
NonOverlapRegionsTest.h |
packedVectorTest |
PackedVectorTest.cpp |
PackedVectorTest.h |
referenceSequenceTest |
ReferenceSequenceTest.cpp |
ReferenceSequenceTest.h |
reusableVector |
ReusableVectorTest.cpp |
ReusableVectorTest.h |
string |
StringTest.cpp |
StringTest.h |
trimSequence |
TrimSequence.cpp |
Chromosome_test.cpp |
GenomeSequence_test.cpp |
GreedyTupleAligner_test.cpp |
gtest.cpp |
STLUtilities_test.cpp |
TrimSequence_test.cpp |
BaseAsciiMap.cpp |
BaseAsciiMap.h |
BaseQualityHelper.cpp |
BaseQualityHelper.h |
BaseUtilities.cpp |
BaseUtilities.h |
BasicHash.cpp |
BasicHash.h |
BgzfFileType.cpp |
BgzfFileType.h |
BgzfFileTypeRecovery.cpp |
BgzfFileTypeRecovery.h |
CharBuffer.cpp |
CharBuffer.h |
Chromosome.cpp |
Chromosome.h |
Cigar.cpp |
Cigar.h |
CigarRoller.cpp |
CigarRoller.h |
Constant.h |
CSG_MD5.h |
Error.cpp |
Error.h |
ErrorHandler.cpp |
ErrorHandler.h |
FileType.cpp |
FileType.h |
FortranFormat.cpp |
FortranFormat.h |
Generic.cpp |
Generic.h |
GenomeSequence.cpp |
GenomeSequence.h |
GenomeSequenceHelpers.h |
GenotypeLists.cpp |
GenotypeLists.h |
glfHandler.cpp |
glfHandler.h |
GreedyTupleAligner.h |
GzipFileType.cpp |
GzipFileType.h |
GzipHeader.cpp |
GzipHeader.h |
Hash.cpp |
Hash.h |
IndexBase.cpp |
IndexBase.h |
InplaceMerge.cpp |
InplaceMerge.h |
Input.cpp |
Input.h |
InputFile.cpp |
InputFile.h |
IntArray.cpp |
IntArray.h |
IntHash.cpp |
IntHash.h |
LongHash.h |
LongInt.h |
LongLongCounter.cpp |
LongLongCounter.h |
MapFunction.cpp |
MapFunction.h |
MathConstant.h |
MathMatrix.cpp |
MathMatrix.h |
MathVector.cpp |
MathVector.h |
MemoryAllocators.cpp |
MemoryAllocators.h |
MemoryInfo.cpp |
MemoryInfo.h |
MemoryMap.cpp |
MemoryMap.h |
MemoryMapArray.cpp |
MemoryMapArray.h |
MiniDeflate.cpp |
MiniDeflate.h |
NonOverlapRegions.cpp |
NonOverlapRegions.h |
PackedVector.h |
Parameters.cpp |
Parameters.h |
Pedigree.cpp |
Pedigree.h |
PedigreeAlleleFreq.cpp |
PedigreeAlleleFreq.h |
PedigreeAlleles.h |
PedigreeDescription.cpp |
PedigreeDescription.h |
PedigreeFamily.cpp |
PedigreeFamily.h |
PedigreeGlobals.cpp |
PedigreeGlobals.h |
PedigreeLoader.cpp |
PedigreePerson.cpp |
PedigreePerson.h |
PedigreeTrim.cpp |
PedigreeTwin.cpp |
Performance.h |
PhoneHome.cpp |
PhoneHome.h |
QuickIndex.cpp |
QuickIndex.h |
Random.cpp |
Random.h |
ReferenceSequence.cpp |
ReferenceSequence.h |
ReusableVector.h |
SimpleStats.h |
SmithWaterman.cpp |
SmithWaterman.h |
Sort.cpp |
Sort.h |
StatGenStatus.cpp |
StatGenStatus.h |
STLUtilities.cpp |
STLUtilities.h |
String.cpp |
StringAlias.cpp |
StringAlias.h |
StringArray.cpp |
StringArray.h |
StringBasics.cpp |
StringBasics.h |
StringHash.cpp |
StringHash.h |
StringMap.cpp |
StringMap.h |
Tabix.cpp |
Tabix.h |
TrimSequence.h |
UncompressedFileType.cpp |
UncompressedFileType.h |
UnitTest.h |
glf |
test |
Main.cpp |
ReadFiles.cpp |
ReadFiles.h |
Validate.cpp |
Validate.h |
WriteFiles.cpp |
WriteFiles.h |
GlfException.cpp |
GlfException.h |
GlfFile.cpp |
GlfFile.h |
GlfHeader.cpp |
GlfHeader.h |
GlfRecord.cpp |
GlfRecord.h |
GlfRefSection.cpp |
GlfRefSection.h |
GlfStatus.cpp |
GlfStatus.h |
samtools |
bam.h |
bgzf.c |
bgzf.h |
khash.h |
knetfile.c |
knetfile.h |