File List

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

[detail level 1234]

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