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 | |