affxparser: Affymetrix File Parsing SDK

Package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, BAR). It provides methods for fast and memory efficient parsing of Affymetrix files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files are supported. Currently, there are methods for reading chip definition file (CDF) and a cell intensity file (CEL). These files can be read either in full or in part. For example, probe signals from a few probesets can be extracted very quickly from a set of CEL files into a convenient list structure.

AuthorHenrik Bengtsson [aut], James Bullard [aut], Robert Gentleman [ctb], Kasper Daniel Hansen [aut, cre], Jim Hester [ctb], Martin Morgan [ctb]
Date of publicationNone
MaintainerKasper Daniel Hansen <kasperdanielhansen@gmail.com>
LicenseLGPL (>= 2)
Version1.46.0
https://github.com/HenrikBengtsson/affxparser

View on Bioconductor

Man pages

1._Dictionary: 1. Dictionary

2._Cell_coordinates_and_cell_indices: 2. Cell coordinates and cell indices

9._Advanced_-_Cell-index_maps_for_reading_and_writing: 9. Advanced - Cell-index maps for reading and writing

affxparser-package: Package affxparser

applyCdfGroupFields: Applies a function to a list of fields of each group in a CDF...

applyCdfGroups: Applies a function over the groups in a CDF structure

arrangeCelFilesByChipType: Moves CEL files to subdirectories with names corresponding to...

cdfAddBaseMmCounts: Adds the number of allele A and allele B mismatching...

cdfAddPlasqTypes: Adds the PLASQ types for the probes in a CDF structure

cdfAddProbeOffsets: Adds probe offsets to the groups in a CDF structure

cdfGetFields: Gets a subset of groups fields in a CDF structure

cdfGetGroups: Gets a subset of groups in a CDF structure

cdfGtypeCelToPQ: Function to immitate Affymetrix' gtype\_cel\_to\_pq software

cdfHeaderToCelHeader: Creates a valid CEL header from a CDF header

cdfMergeAlleles: Function to join CDF allele A and allele B groups strand by...

cdfMergeStrands: Function to join CDF groups with the same names

cdfMergeToQuartets: Function to re-arrange CDF groups values in quartets

cdfOrderBy: Orders the fields according to the value of another field in...

cdfOrderColumnsBy: Orders the columns of fields according to the values in a...

cdfSetDimension: Sets the dimension of an object

compareCdfs: Compares the contents of two CDF files

compareCels: Compares the contents of two CEL files

convertCdf: Converts a CDF into the same CDF but with another format

convertCel: Converts a CEL into the same CEL but with another format

copyCel: Copies a CEL file

createCel: Creates an empty CEL file

findCdf: Search for CDF files in multiple directories

findFiles: Finds one or several files in multiple directories

invertMap: Inverts a read or a write map

isCelFile: Checks if a file is a CEL file or not

parseDatHeaderString: Parses a DAT header string

readBpmap: Parses a Bpmap file

readCcg: Reads an Affymetrix Command Console Generic (CCG) Data file

readCcgHeader: Reads an the header of an Affymetrix Command Console Generic...

readCdf: Parsing a CDF file using Affymetrix Fusion SDK

readCdfCellIndices: Reads (one-based) cell indices of units (probesets) in an...

readCdfDataFrame: Reads units (probesets) from an Affymetrix CDF file

readCdfGroupNames: Reads group names for a set of units (probesets) in an...

readCdfHeader: Reads the header associated with an Affymetrix CDF file

readCdfIsPm: Checks if cells in a CDF file are perfect-match probes or not

readCdfNbrOfCellsPerUnitGroup: Gets the number of cells (probes) that each group of each...

readCdfQc: Reads the QC units of CDF file

readCdfUnitNames: Reads unit (probeset) names from an Affymetrix CDF file

readCdfUnits: Reads units (probesets) from an Affymetrix CDF file

readCdfUnitsWriteMap: Generates an Affymetrix cell-index write map from a CDF file

readCel: Reads an Affymetrix CEL file

readCelHeader: Parsing the header of an Affymetrix CEL file

readCelIntensities: Reads the intensities contained in several Affymetrix CEL...

readCelRectangle: Reads a spatial subset of probe-level data from Affymetrix...

readCelUnits: Reads probe-level data ordered as units (probesets) from one...

readChp: A function to read Affymetrix CHP files

readClf: Parsing a CLF file using Affymetrix Fusion SDK

readClfEnv: Parsing a CLF file using Affymetrix Fusion SDK

readClfHeader: Read the header of a CLF file.

readPgf: Parsing a PGF file using Affymetrix Fusion SDK

readPgfEnv: Parsing a PGF file using Affymetrix Fusion SDK

readPgfHeader: Read the header of a PGF file into a list.

updateCel: Updates a CEL file

updateCelUnits: Updates a CEL file unit by unit

writeCdf: Creates a binary CDF file

writeCdfHeader: Writes a CDF header

writeCdfQcUnits: Writes CDF QC units

writeCdfUnits: Writes CDF units

writeCelHeader: Writes a CEL header to a connection

writeTpmap: Writes BPMAP and TPMAP files.

Functions

1. Dictionary Man page
2. Cell coordinates and cell indices Man page
9. Advanced - Cell-index maps for reading and writing Man page
affxparser Man page
affxparser-package Man page
applyCdfBlocks Man page
applyCdfGroupFields Man page
applyCdfGroups Man page
arrangeCelFilesByChipType Man page
cdfAddBaseMmCounts Man page
cdfAddPlasqTypes Man page
cdfAddProbeOffsets Man page
cdfGetFields Man page
cdfGetGroups Man page
cdfGtypeCelToPQ Man page
cdfHeaderToCelHeader Man page
cdfMergeAlleles Man page
cdfMergeStrands Man page
cdfMergeToQuartets Man page
cdfOrderBy Man page
cdfOrderColumnsBy Man page
cdfSetDimension Man page
compareCdfs Man page
compareCels Man page
convertCdf Man page
convertCel Man page
copyCel Man page
createCel Man page
findCdf Man page
findFiles Man page
invertMap Man page
isCelFile Man page
parseDatHeaderString Man page
readBpmap Man page
readBpmapHeader Man page
readBpmapSeqinfo Man page
readCcg Man page
readCcgHeader Man page
readCdf Man page
readCdfCellIndices Man page
readCdfDataFrame Man page
readCdfGroupNames Man page
readCdfHeader Man page
readCdfIsPm Man page
readCdfNbrOfCellsPerUnitGroup Man page
readCdfQc Man page
readCdfUnitNames Man page
readCdfUnits Man page
readCdfUnitsWriteMap Man page
readCel Man page
readCelHeader Man page
readCelIntensities Man page
readCelRectangle Man page
readCelUnits Man page
readChp Man page
readClf Man page
readClfEnv Man page
readClfHeader Man page
readPgf Man page
readPgfEnv Man page
readPgfHeader Man page
tpmap2bpmap Man page
updateCel Man page
updateCelUnits Man page
writeCdf Man page
writeCdfHeader Man page
writeCdfQcUnits Man page
writeCdfUnits Man page
writeCelHeader Man page
writeTpmap Man page

Files

affxparser/DESCRIPTION
affxparser/NAMESPACE
affxparser/NEWS
affxparser/R
affxparser/R/901.Dictionary.R affxparser/R/902.CellCoordinatesAndIndices.R affxparser/R/909.CellIndexMaps.R affxparser/R/applyCdfBlocks.R affxparser/R/applyCdfGroupFields.R affxparser/R/applyCdfGroups.R affxparser/R/arrangeCelFilesByChipType.R affxparser/R/cdfAddBaseMmCounts.R affxparser/R/cdfAddPlasqTypes.R affxparser/R/cdfAddProbeOffsets.R affxparser/R/cdfGetFields.R affxparser/R/cdfGetGroups.R affxparser/R/cdfGtypeCelToPQ.R affxparser/R/cdfHeaderToCelHeader.R affxparser/R/cdfMergeAlleles.R affxparser/R/cdfMergeStrands.R affxparser/R/cdfMergeToQuartets.R affxparser/R/cdfOrderBy.R affxparser/R/cdfOrderColumnsBy.R affxparser/R/cdfSetDimension.R affxparser/R/compareCdfs.R affxparser/R/compareCels.R affxparser/R/convertCdf.R affxparser/R/convertCel.R affxparser/R/copyCel.R affxparser/R/createCel.R affxparser/R/findCdf.R affxparser/R/findFiles.R affxparser/R/invertMap.R affxparser/R/isCelFile.R affxparser/R/parseDatHeaderString.R affxparser/R/private.assertMap.R affxparser/R/private.readCelHeaderV3.R affxparser/R/private.readCelHeaderV4.R affxparser/R/private.unwrapCelHeaderV4.R affxparser/R/private.wrapCelHeaderV4.R affxparser/R/readBpmap.R affxparser/R/readBpmapHeader.R affxparser/R/readBpmapSeqInfo.R affxparser/R/readCcg.R affxparser/R/readCcgHeader.R affxparser/R/readCdf.R affxparser/R/readCdfCellIndices.R affxparser/R/readCdfDataFrame.R affxparser/R/readCdfGroupNames.R affxparser/R/readCdfHeader.R affxparser/R/readCdfIsPm.R affxparser/R/readCdfNbrOfCellsPerUnitGroup.R affxparser/R/readCdfQc.R affxparser/R/readCdfUnitNames.R affxparser/R/readCdfUnits.R affxparser/R/readCdfUnitsWriteMap.R affxparser/R/readCel.R affxparser/R/readCelHeader.R affxparser/R/readCelIntensities.R affxparser/R/readCelRectangle.R affxparser/R/readCelUnits.R affxparser/R/readChp.R affxparser/R/readClf.R affxparser/R/readPgf.R affxparser/R/testWriteAndReadEmptyCdf.R affxparser/R/testWriteAndReadEmptyCel.R affxparser/R/tpmap2bpmap.R affxparser/R/traverseCcg.R affxparser/R/updateCel.R affxparser/R/updateCelUnits.R affxparser/R/writeCcg.R affxparser/R/writeCdf.R affxparser/R/writeCdf.private.R affxparser/R/writeCdfHeader.R affxparser/R/writeCdfQcUnits.R affxparser/R/writeCdfUnits.R affxparser/R/writeCelHeader.R affxparser/R/writeTpmap.R affxparser/R/zzz.R
affxparser/cleanup
affxparser/inst
affxparser/inst/extras
affxparser/inst/extras/easternEgg.gz
affxparser/inst/info
affxparser/inst/info/Makefile
affxparser/inst/info/changes2fusion.txt
affxparser/inst/info/fusion_1.1.0_patches
affxparser/inst/info/fusion_1.1.0_patches/AffxByteArray.cpp-patch
affxparser/inst/info/fusion_1.1.0_patches/AffxConv.cpp-patch
affxparser/inst/info/fusion_1.1.0_patches/AffymetrixBaseTypes.h-patch
affxparser/inst/info/fusion_1.1.0_patches/CDFFileData.cpp-patch
affxparser/inst/info/fusion_1.1.0_patches/affy-base-types.h-patch
affxparser/inst/info/fusion_1.1.0_patches/gcc-4.7.cpp-patch
affxparser/inst/info/fusion_1.1.2_patches
affxparser/inst/info/fusion_1.1.2_patches/AffxByteArray.cpp-patch
affxparser/inst/info/fusion_1.1.2_patches/AffxConv.cpp-patch
affxparser/inst/info/fusion_1.1.2_patches/AffxConv.cpp-patch2
affxparser/inst/info/fusion_1.1.2_patches/AffymetrixBaseTypes.h-patch
affxparser/inst/info/fusion_1.1.2_patches/CDFFileData.cpp-patch
affxparser/inst/info/fusion_1.1.2_patches/CELFileData.h-patch
affxparser/inst/info/fusion_1.1.2_patches/CHPMultiDataData.cpp-patch
affxparser/inst/info/fusion_1.1.2_patches/FileUtils.cpp-patch
affxparser/inst/info/fusion_1.1.2_patches/Fs.cpp-patch
affxparser/inst/info/fusion_1.1.2_patches/TsvFile.cpp-patch
affxparser/inst/info/fusion_1.1.2_patches/Util.cpp-patch
affxparser/inst/info/fusion_1.1.2_patches/Verbose.cpp-patch
affxparser/inst/info/fusion_1.1.2_patches/affy-base-types.h-patch
affxparser/inst/info/fusion_sdk_license.html
affxparser/inst/testscripts
affxparser/inst/testscripts/manualTest.R
affxparser/inst/testscripts/speedtest.R
affxparser/inst/testscripts/writeAndReadEmptyCdf.R
affxparser/inst/testscripts/writeAndReadEmptyCel.R
affxparser/man
affxparser/man/1._Dictionary.Rd affxparser/man/2._Cell_coordinates_and_cell_indices.Rd affxparser/man/9._Advanced_-_Cell-index_maps_for_reading_and_writing.Rd affxparser/man/affxparser-package.Rd affxparser/man/applyCdfGroupFields.Rd affxparser/man/applyCdfGroups.Rd affxparser/man/arrangeCelFilesByChipType.Rd affxparser/man/cdfAddBaseMmCounts.Rd affxparser/man/cdfAddPlasqTypes.Rd affxparser/man/cdfAddProbeOffsets.Rd affxparser/man/cdfGetFields.Rd affxparser/man/cdfGetGroups.Rd affxparser/man/cdfGtypeCelToPQ.Rd affxparser/man/cdfHeaderToCelHeader.Rd affxparser/man/cdfMergeAlleles.Rd affxparser/man/cdfMergeStrands.Rd affxparser/man/cdfMergeToQuartets.Rd affxparser/man/cdfOrderBy.Rd affxparser/man/cdfOrderColumnsBy.Rd affxparser/man/cdfSetDimension.Rd affxparser/man/compareCdfs.Rd affxparser/man/compareCels.Rd affxparser/man/convertCdf.Rd affxparser/man/convertCel.Rd affxparser/man/copyCel.Rd affxparser/man/createCel.Rd affxparser/man/findCdf.Rd affxparser/man/findFiles.Rd affxparser/man/invertMap.Rd affxparser/man/isCelFile.Rd affxparser/man/parseDatHeaderString.Rd affxparser/man/readBpmap.Rd affxparser/man/readCcg.Rd affxparser/man/readCcgHeader.Rd affxparser/man/readCdf.Rd affxparser/man/readCdfCellIndices.Rd affxparser/man/readCdfDataFrame.Rd affxparser/man/readCdfGroupNames.Rd affxparser/man/readCdfHeader.Rd affxparser/man/readCdfIsPm.Rd affxparser/man/readCdfNbrOfCellsPerUnitGroup.Rd affxparser/man/readCdfQc.Rd affxparser/man/readCdfUnitNames.Rd affxparser/man/readCdfUnits.Rd affxparser/man/readCdfUnitsWriteMap.Rd affxparser/man/readCel.Rd affxparser/man/readCelHeader.Rd affxparser/man/readCelIntensities.Rd affxparser/man/readCelRectangle.Rd affxparser/man/readCelUnits.Rd affxparser/man/readChp.Rd affxparser/man/readClf.Rd affxparser/man/readClfEnv.Rd affxparser/man/readClfHeader.Rd affxparser/man/readPgf.Rd affxparser/man/readPgfEnv.Rd affxparser/man/readPgfHeader.Rd affxparser/man/updateCel.Rd affxparser/man/updateCelUnits.Rd affxparser/man/writeCdf.Rd affxparser/man/writeCdfHeader.Rd affxparser/man/writeCdfQcUnits.Rd affxparser/man/writeCdfUnits.Rd affxparser/man/writeCelHeader.Rd affxparser/man/writeTpmap.Rd
affxparser/src
affxparser/src/Makevars
affxparser/src/Makevars.win
affxparser/src/RAffxErrHandler.h
affxparser/src/R_affx_bpmap_parser.cpp
affxparser/src/R_affx_cdf_extras.cpp
affxparser/src/R_affx_cdf_extras.h
affxparser/src/R_affx_cdf_parser.cpp
affxparser/src/R_affx_cel_parser.cpp
affxparser/src/R_affx_chp_parser.cpp
affxparser/src/R_affx_clf_pgf_parser.cpp
affxparser/src/R_affx_constants.h
affxparser/src/R_affx_test_bpmap_cmdline.cpp
affxparser/src/R_affx_test_cdfwriter_cmdline.cpp
affxparser/src/R_affx_test_celwriter_cmdline.cpp
affxparser/src/R_affx_test_cmd_line.cpp
affxparser/src/_mingw.h
affxparser/src/_mingw_gcc463.h
affxparser/src/_mingw_gcc493.h
affxparser/src/fusion_sdk
affxparser/src/fusion_sdk/calvin_files
affxparser/src/fusion_sdk/calvin_files/array
affxparser/src/fusion_sdk/calvin_files/array/src
affxparser/src/fusion_sdk/calvin_files/array/src/ArrayAttributes.cpp
affxparser/src/fusion_sdk/calvin_files/array/src/ArrayAttributes.h
affxparser/src/fusion_sdk/calvin_files/array/src/ArrayAudit.cpp
affxparser/src/fusion_sdk/calvin_files/array/src/ArrayAudit.h
affxparser/src/fusion_sdk/calvin_files/array/src/ArrayAuditActionTypes.h
affxparser/src/fusion_sdk/calvin_files/array/src/ArrayData.cpp
affxparser/src/fusion_sdk/calvin_files/array/src/ArrayData.h
affxparser/src/fusion_sdk/calvin_files/array/src/ArrayId.h
affxparser/src/fusion_sdk/calvin_files/array/src/ArrayMedia.cpp
affxparser/src/fusion_sdk/calvin_files/array/src/ArrayMedia.h
affxparser/src/fusion_sdk/calvin_files/array/src/CreateStep.cpp
affxparser/src/fusion_sdk/calvin_files/array/src/CreateStep.h
affxparser/src/fusion_sdk/calvin_files/array/src/PATAssignment.cpp
affxparser/src/fusion_sdk/calvin_files/array/src/PATAssignment.h
affxparser/src/fusion_sdk/calvin_files/data
affxparser/src/fusion_sdk/calvin_files/data/src
affxparser/src/fusion_sdk/calvin_files/data/src/AllelePeaks.h
affxparser/src/fusion_sdk/calvin_files/data/src/CDFData.cpp
affxparser/src/fusion_sdk/calvin_files/data/src/CDFData.h
affxparser/src/fusion_sdk/calvin_files/data/src/CDFDataTypes.h
affxparser/src/fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.cpp
affxparser/src/fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.h
affxparser/src/fusion_sdk/calvin_files/data/src/CDFProbeInformation.cpp
affxparser/src/fusion_sdk/calvin_files/data/src/CDFProbeInformation.h
affxparser/src/fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.cpp
affxparser/src/fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h
affxparser/src/fusion_sdk/calvin_files/data/src/CDFQCProbeInformation.cpp
affxparser/src/fusion_sdk/calvin_files/data/src/CDFQCProbeInformation.h
affxparser/src/fusion_sdk/calvin_files/data/src/CDFQCProbeSetInformation.cpp
affxparser/src/fusion_sdk/calvin_files/data/src/CDFQCProbeSetInformation.h
affxparser/src/fusion_sdk/calvin_files/data/src/CELData.cpp
affxparser/src/fusion_sdk/calvin_files/data/src/CELData.h
affxparser/src/fusion_sdk/calvin_files/data/src/CHPBackgroundZone.cpp
affxparser/src/fusion_sdk/calvin_files/data/src/CHPBackgroundZone.h
affxparser/src/fusion_sdk/calvin_files/data/src/CHPData.cpp
affxparser/src/fusion_sdk/calvin_files/data/src/CHPData.h
affxparser/src/fusion_sdk/calvin_files/data/src/CHPExpressionEntry.cpp
affxparser/src/fusion_sdk/calvin_files/data/src/CHPExpressionEntry.h
affxparser/src/fusion_sdk/calvin_files/data/src/CHPGenotypeEntry.cpp
affxparser/src/fusion_sdk/calvin_files/data/src/CHPGenotypeEntry.h
affxparser/src/fusion_sdk/calvin_files/data/src/CHPMultiDataData.cpp
affxparser/src/fusion_sdk/calvin_files/data/src/CHPMultiDataData.h
affxparser/src/fusion_sdk/calvin_files/data/src/CHPQuantificationData.cpp
affxparser/src/fusion_sdk/calvin_files/data/src/CHPQuantificationData.h
affxparser/src/fusion_sdk/calvin_files/data/src/CHPQuantificationDetectionData.cpp
affxparser/src/fusion_sdk/calvin_files/data/src/CHPQuantificationDetectionData.h
affxparser/src/fusion_sdk/calvin_files/data/src/CHPReseqEntry.h
affxparser/src/fusion_sdk/calvin_files/data/src/CHPTilingData.cpp
affxparser/src/fusion_sdk/calvin_files/data/src/CHPTilingData.h
affxparser/src/fusion_sdk/calvin_files/data/src/CHPTilingEntry.h
affxparser/src/fusion_sdk/calvin_files/data/src/CHPUniversalEntry.cpp
affxparser/src/fusion_sdk/calvin_files/data/src/CHPUniversalEntry.h
affxparser/src/fusion_sdk/calvin_files/data/src/ChromosomeMultiDataSummaryData.h
affxparser/src/fusion_sdk/calvin_files/data/src/ChromosomeSegmentMultiDataData.h
affxparser/src/fusion_sdk/calvin_files/data/src/ColumnInfo.cpp
affxparser/src/fusion_sdk/calvin_files/data/src/ColumnInfo.h
affxparser/src/fusion_sdk/calvin_files/data/src/CytoGenotypeCallMultiDataData.h
affxparser/src/fusion_sdk/calvin_files/data/src/DATData.cpp
affxparser/src/fusion_sdk/calvin_files/data/src/DATData.h
affxparser/src/fusion_sdk/calvin_files/data/src/DataException.cpp
affxparser/src/fusion_sdk/calvin_files/data/src/DataException.h
affxparser/src/fusion_sdk/calvin_files/data/src/DataGroup.cpp
affxparser/src/fusion_sdk/calvin_files/data/src/DataGroup.h
affxparser/src/fusion_sdk/calvin_files/data/src/DataGroupHeader.cpp
affxparser/src/fusion_sdk/calvin_files/data/src/DataGroupHeader.h
affxparser/src/fusion_sdk/calvin_files/data/src/DataSet.cpp
affxparser/src/fusion_sdk/calvin_files/data/src/DataSet.h
affxparser/src/fusion_sdk/calvin_files/data/src/DataSetHeader.cpp
affxparser/src/fusion_sdk/calvin_files/data/src/DataSetHeader.h
affxparser/src/fusion_sdk/calvin_files/data/src/FamilialMultiDataData.h
affxparser/src/fusion_sdk/calvin_files/data/src/FileHeader.cpp
affxparser/src/fusion_sdk/calvin_files/data/src/FileHeader.h
affxparser/src/fusion_sdk/calvin_files/data/src/GenericData.cpp
affxparser/src/fusion_sdk/calvin_files/data/src/GenericData.h
affxparser/src/fusion_sdk/calvin_files/data/src/GenericDataHeader.cpp
affxparser/src/fusion_sdk/calvin_files/data/src/GenericDataHeader.h
affxparser/src/fusion_sdk/calvin_files/data/src/GenericDataTypes.h
affxparser/src/fusion_sdk/calvin_files/data/src/MarkerABSignals.h
affxparser/src/fusion_sdk/calvin_files/data/src/MemMapFile.cpp
affxparser/src/fusion_sdk/calvin_files/data/src/MemMapFile.h
affxparser/src/fusion_sdk/calvin_files/data/src/ProbeSetMultiDataData.cpp
affxparser/src/fusion_sdk/calvin_files/data/src/ProbeSetMultiDataData.h
affxparser/src/fusion_sdk/calvin_files/data/src/ProbeSetQuantificationData.h
affxparser/src/fusion_sdk/calvin_files/data/src/ProbeSetQuantificationDetectionData.h
affxparser/src/fusion_sdk/calvin_files/data/src/TilingResultData.h
affxparser/src/fusion_sdk/calvin_files/exception
affxparser/src/fusion_sdk/calvin_files/exception/src
affxparser/src/fusion_sdk/calvin_files/exception/src/DevelopmentException.cpp
affxparser/src/fusion_sdk/calvin_files/exception/src/DevelopmentException.h
affxparser/src/fusion_sdk/calvin_files/exception/src/ExceptionBase.cpp
affxparser/src/fusion_sdk/calvin_files/exception/src/ExceptionBase.h
affxparser/src/fusion_sdk/calvin_files/exception/src/InterpretationException.cpp
affxparser/src/fusion_sdk/calvin_files/exception/src/InterpretationException.h
affxparser/src/fusion_sdk/calvin_files/fusion
affxparser/src/fusion_sdk/calvin_files/fusion/src
affxparser/src/fusion_sdk/calvin_files/fusion/src/CalvinAdapter
affxparser/src/fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.cpp
affxparser/src/fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.h
affxparser/src/fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.cpp
affxparser/src/fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.h
affxparser/src/fusion_sdk/calvin_files/fusion/src/FusionArrayFileReader.cpp
affxparser/src/fusion_sdk/calvin_files/fusion/src/FusionArrayFileReader.h
affxparser/src/fusion_sdk/calvin_files/fusion/src/FusionBARData.cpp
affxparser/src/fusion_sdk/calvin_files/fusion/src/FusionBARData.h
affxparser/src/fusion_sdk/calvin_files/fusion/src/FusionBEDData.cpp
affxparser/src/fusion_sdk/calvin_files/fusion/src/FusionBEDData.h
affxparser/src/fusion_sdk/calvin_files/fusion/src/FusionBPMAPData.cpp
affxparser/src/fusion_sdk/calvin_files/fusion/src/FusionBPMAPData.h
affxparser/src/fusion_sdk/calvin_files/fusion/src/FusionCDFData.cpp
affxparser/src/fusion_sdk/calvin_files/fusion/src/FusionCDFData.h
affxparser/src/fusion_sdk/calvin_files/fusion/src/FusionCDFQCProbeSetNames.cpp
affxparser/src/fusion_sdk/calvin_files/fusion/src/FusionCDFQCProbeSetNames.h
affxparser/src/fusion_sdk/calvin_files/fusion/src/FusionCELData.cpp
affxparser/src/fusion_sdk/calvin_files/fusion/src/FusionCELData.h
affxparser/src/fusion_sdk/calvin_files/fusion/src/FusionCELDataAdapterInterface.h
affxparser/src/fusion_sdk/calvin_files/fusion/src/FusionCHPData.cpp
affxparser/src/fusion_sdk/calvin_files/fusion/src/FusionCHPData.h
affxparser/src/fusion_sdk/calvin_files/fusion/src/FusionCHPDataAdapterInterface.h
affxparser/src/fusion_sdk/calvin_files/fusion/src/FusionCHPGenericData.cpp
affxparser/src/fusion_sdk/calvin_files/fusion/src/FusionCHPGenericData.h
affxparser/src/fusion_sdk/calvin_files/fusion/src/FusionCHPLegacyData.cpp
affxparser/src/fusion_sdk/calvin_files/fusion/src/FusionCHPLegacyData.h
affxparser/src/fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataAccessor.cpp
affxparser/src/fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataAccessor.h
affxparser/src/fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataData.cpp
affxparser/src/fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataData.h
affxparser/src/fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationData.cpp
affxparser/src/fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationData.h
affxparser/src/fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationDetectionData.cpp
affxparser/src/fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationDetectionData.h
affxparser/src/fusion_sdk/calvin_files/fusion/src/FusionCHPTilingData.cpp
affxparser/src/fusion_sdk/calvin_files/fusion/src/FusionCHPTilingData.h
affxparser/src/fusion_sdk/calvin_files/fusion/src/FusionCoords.h
affxparser/src/fusion_sdk/calvin_files/fusion/src/FusionGRDData.cpp
affxparser/src/fusion_sdk/calvin_files/fusion/src/FusionGRDData.h
affxparser/src/fusion_sdk/calvin_files/fusion/src/FusionGrcFileReader.cpp
affxparser/src/fusion_sdk/calvin_files/fusion/src/FusionGrcFileReader.h
affxparser/src/fusion_sdk/calvin_files/fusion/src/FusionMSKData.cpp
affxparser/src/fusion_sdk/calvin_files/fusion/src/FusionMSKData.h
affxparser/src/fusion_sdk/calvin_files/fusion/src/FusionPSIData.cpp
affxparser/src/fusion_sdk/calvin_files/fusion/src/FusionPSIData.h
affxparser/src/fusion_sdk/calvin_files/fusion/src/FusionProbeSetResults.cpp
affxparser/src/fusion_sdk/calvin_files/fusion/src/FusionProbeSetResults.h
affxparser/src/fusion_sdk/calvin_files/fusion/src/FusionSMDData.cpp
affxparser/src/fusion_sdk/calvin_files/fusion/src/FusionSMDData.h
affxparser/src/fusion_sdk/calvin_files/fusion/src/FusionTagValuePairType.h
affxparser/src/fusion_sdk/calvin_files/fusion/src/GCOSAdapter
affxparser/src/fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.cpp
affxparser/src/fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.h
affxparser/src/fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.cpp
affxparser/src/fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.h
affxparser/src/fusion_sdk/calvin_files/fusion/src/fusionexception.h
affxparser/src/fusion_sdk/calvin_files/parameter
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affxparser/src/fusion_sdk/calvin_files/parameter/src/AffymetrixParameterConsts.h
affxparser/src/fusion_sdk/calvin_files/parameter/src/CELAlgorithmParameterNames.h
affxparser/src/fusion_sdk/calvin_files/parameter/src/Parameter.h
affxparser/src/fusion_sdk/calvin_files/parameter/src/ParameterException.cpp
affxparser/src/fusion_sdk/calvin_files/parameter/src/ParameterException.h
affxparser/src/fusion_sdk/calvin_files/parameter/src/ParameterFileData.cpp
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affxparser/src/fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.cpp
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affxparser/src/fusion_sdk/calvin_files/parsers
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affxparser/src/fusion_sdk/calvin_files/parsers/src/ArrayFileReader.cpp
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affxparser/src/fusion_sdk/calvin_files/parsers/src/AuditFileConstants.h
affxparser/src/fusion_sdk/calvin_files/parsers/src/AuditFileReader.cpp
affxparser/src/fusion_sdk/calvin_files/parsers/src/AuditFileReader.h
affxparser/src/fusion_sdk/calvin_files/parsers/src/CDFFileReader.cpp
affxparser/src/fusion_sdk/calvin_files/parsers/src/CDFFileReader.h
affxparser/src/fusion_sdk/calvin_files/parsers/src/CHPFileReader.cpp
affxparser/src/fusion_sdk/calvin_files/parsers/src/CHPFileReader.h
affxparser/src/fusion_sdk/calvin_files/parsers/src/CHPMultiDataFileReader.cpp
affxparser/src/fusion_sdk/calvin_files/parsers/src/CHPMultiDataFileReader.h
affxparser/src/fusion_sdk/calvin_files/parsers/src/CHPQuantificationDetectionFileReader.cpp
affxparser/src/fusion_sdk/calvin_files/parsers/src/CHPQuantificationDetectionFileReader.h
affxparser/src/fusion_sdk/calvin_files/parsers/src/CHPQuantificationFileReader.cpp
affxparser/src/fusion_sdk/calvin_files/parsers/src/CHPQuantificationFileReader.h
affxparser/src/fusion_sdk/calvin_files/parsers/src/CHPTilingFileReader.cpp
affxparser/src/fusion_sdk/calvin_files/parsers/src/CHPTilingFileReader.h
affxparser/src/fusion_sdk/calvin_files/parsers/src/CelFileReader.cpp
affxparser/src/fusion_sdk/calvin_files/parsers/src/CelFileReader.h
affxparser/src/fusion_sdk/calvin_files/parsers/src/DATFileReader.cpp
affxparser/src/fusion_sdk/calvin_files/parsers/src/DATFileReader.h
affxparser/src/fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.cpp
affxparser/src/fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.h
affxparser/src/fusion_sdk/calvin_files/parsers/src/DataGroupReader.cpp
affxparser/src/fusion_sdk/calvin_files/parsers/src/DataGroupReader.h
affxparser/src/fusion_sdk/calvin_files/parsers/src/DataSetHeaderReader.cpp
affxparser/src/fusion_sdk/calvin_files/parsers/src/DataSetHeaderReader.h
affxparser/src/fusion_sdk/calvin_files/parsers/src/DataSetReader.cpp
affxparser/src/fusion_sdk/calvin_files/parsers/src/DataSetReader.h
affxparser/src/fusion_sdk/calvin_files/parsers/src/FileException.cpp
affxparser/src/fusion_sdk/calvin_files/parsers/src/FileException.h
affxparser/src/fusion_sdk/calvin_files/parsers/src/FileHeaderReader.cpp
affxparser/src/fusion_sdk/calvin_files/parsers/src/FileHeaderReader.h
affxparser/src/fusion_sdk/calvin_files/parsers/src/FileInput.cpp
affxparser/src/fusion_sdk/calvin_files/parsers/src/FileInput.h
affxparser/src/fusion_sdk/calvin_files/parsers/src/GenericDataHeaderReader.cpp
affxparser/src/fusion_sdk/calvin_files/parsers/src/GenericDataHeaderReader.h
affxparser/src/fusion_sdk/calvin_files/parsers/src/GenericFileReader.cpp
affxparser/src/fusion_sdk/calvin_files/parsers/src/GenericFileReader.h
affxparser/src/fusion_sdk/calvin_files/parsers/src/GridControlFileReader.cpp
affxparser/src/fusion_sdk/calvin_files/parsers/src/GridControlFileReader.h
affxparser/src/fusion_sdk/calvin_files/parsers/src/ParameterFileReader.cpp
affxparser/src/fusion_sdk/calvin_files/parsers/src/ParameterFileReader.h
affxparser/src/fusion_sdk/calvin_files/parsers/src/SAXArrayHandlers.cpp
affxparser/src/fusion_sdk/calvin_files/parsers/src/SAXArrayHandlers.h
affxparser/src/fusion_sdk/calvin_files/parsers/src/SAXParameterFileHandlers.cpp
affxparser/src/fusion_sdk/calvin_files/parsers/src/SAXParameterFileHandlers.h
affxparser/src/fusion_sdk/calvin_files/parsers/src/SAXTemplateHandlers.cpp
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affxparser/src/fusion_sdk/calvin_files/parsers/src/TemplateFileReader.cpp
affxparser/src/fusion_sdk/calvin_files/parsers/src/TemplateFileReader.h
affxparser/src/fusion_sdk/calvin_files/parsers/src/TextFileReader.cpp
affxparser/src/fusion_sdk/calvin_files/parsers/src/TextFileReader.h
affxparser/src/fusion_sdk/calvin_files/portability
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affxparser/src/fusion_sdk/calvin_files/portability/src/AffymetrixBaseTypes.h
affxparser/src/fusion_sdk/calvin_files/template
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affxparser/src/fusion_sdk/calvin_files/template/src/TemplateData.cpp
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affxparser/src/fusion_sdk/calvin_files/template/src/TemplateId.h
affxparser/src/fusion_sdk/calvin_files/utils
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affxparser/src/fusion_sdk/calvin_files/utils/src/AffyStlCollectionTypes.h
affxparser/src/fusion_sdk/calvin_files/utils/src/AffymetrixGuid.cpp
affxparser/src/fusion_sdk/calvin_files/utils/src/AffymetrixGuid.h
affxparser/src/fusion_sdk/calvin_files/utils/src/Calvin.cpp
affxparser/src/fusion_sdk/calvin_files/utils/src/Calvin.h
affxparser/src/fusion_sdk/calvin_files/utils/src/Coords.h
affxparser/src/fusion_sdk/calvin_files/utils/src/DateTime.cpp
affxparser/src/fusion_sdk/calvin_files/utils/src/DateTime.h
affxparser/src/fusion_sdk/calvin_files/utils/src/FileUtils.cpp
affxparser/src/fusion_sdk/calvin_files/utils/src/FileUtils.h
affxparser/src/fusion_sdk/calvin_files/utils/src/GenoCallCoder.cpp
affxparser/src/fusion_sdk/calvin_files/utils/src/GenoCallCoder.h
affxparser/src/fusion_sdk/calvin_files/utils/src/StringUtils.cpp
affxparser/src/fusion_sdk/calvin_files/utils/src/StringUtils.h
affxparser/src/fusion_sdk/calvin_files/utils/src/Subgrids.h
affxparser/src/fusion_sdk/calvin_files/utils/src/checksum.cpp
affxparser/src/fusion_sdk/calvin_files/utils/src/checksum.h
affxparser/src/fusion_sdk/calvin_files/writers
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affxparser/src/fusion_sdk/calvin_files/writers/src/ArrayFileWriter.cpp
affxparser/src/fusion_sdk/calvin_files/writers/src/ArrayFileWriter.h
affxparser/src/fusion_sdk/calvin_files/writers/src/AuditFileWriter.cpp
affxparser/src/fusion_sdk/calvin_files/writers/src/AuditFileWriter.h
affxparser/src/fusion_sdk/calvin_files/writers/src/CDFCntrlFileWriter.cpp
affxparser/src/fusion_sdk/calvin_files/writers/src/CDFCntrlFileWriter.h
affxparser/src/fusion_sdk/calvin_files/writers/src/CDFCntrlProbeSetWriter.cpp
affxparser/src/fusion_sdk/calvin_files/writers/src/CDFCntrlProbeSetWriter.h
affxparser/src/fusion_sdk/calvin_files/writers/src/CDFFileWriter.cpp
affxparser/src/fusion_sdk/calvin_files/writers/src/CDFFileWriter.h
affxparser/src/fusion_sdk/calvin_files/writers/src/CDFProbeSetWriter.cpp
affxparser/src/fusion_sdk/calvin_files/writers/src/CDFProbeSetWriter.h
affxparser/src/fusion_sdk/calvin_files/writers/src/CalvinCHPFileBufferWriter.cpp
affxparser/src/fusion_sdk/calvin_files/writers/src/CalvinCHPFileBufferWriter.h
affxparser/src/fusion_sdk/calvin_files/writers/src/CalvinCHPFileUpdater.cpp
affxparser/src/fusion_sdk/calvin_files/writers/src/CalvinCHPFileUpdater.h
affxparser/src/fusion_sdk/calvin_files/writers/src/CalvinCHPFileWriter.cpp
affxparser/src/fusion_sdk/calvin_files/writers/src/CalvinCHPFileWriter.h
affxparser/src/fusion_sdk/calvin_files/writers/src/CalvinCHPMultiDataFileBufferWriter.cpp
affxparser/src/fusion_sdk/calvin_files/writers/src/CalvinCHPMultiDataFileBufferWriter.h
affxparser/src/fusion_sdk/calvin_files/writers/src/CalvinCHPMultiDataFileUpdater.cpp
affxparser/src/fusion_sdk/calvin_files/writers/src/CalvinCHPMultiDataFileUpdater.h
affxparser/src/fusion_sdk/calvin_files/writers/src/CalvinCHPMultiDataFileWriter.cpp
affxparser/src/fusion_sdk/calvin_files/writers/src/CalvinCHPMultiDataFileWriter.h
affxparser/src/fusion_sdk/calvin_files/writers/src/CalvinCHPQuantificationDetectionFileBufferWriter.cpp
affxparser/src/fusion_sdk/calvin_files/writers/src/CalvinCHPQuantificationDetectionFileBufferWriter.h
affxparser/src/fusion_sdk/calvin_files/writers/src/CalvinCHPQuantificationDetectionFileUpdater.cpp
affxparser/src/fusion_sdk/calvin_files/writers/src/CalvinCHPQuantificationDetectionFileUpdater.h
affxparser/src/fusion_sdk/calvin_files/writers/src/CalvinCHPQuantificationDetectionFileWriter.cpp
affxparser/src/fusion_sdk/calvin_files/writers/src/CalvinCHPQuantificationDetectionFileWriter.h
affxparser/src/fusion_sdk/calvin_files/writers/src/CalvinCHPQuantificationFileBufferWriter.cpp
affxparser/src/fusion_sdk/calvin_files/writers/src/CalvinCHPQuantificationFileBufferWriter.h
affxparser/src/fusion_sdk/calvin_files/writers/src/CalvinCHPQuantificationFileUpdater.cpp
affxparser/src/fusion_sdk/calvin_files/writers/src/CalvinCHPQuantificationFileUpdater.h
affxparser/src/fusion_sdk/calvin_files/writers/src/CalvinCHPQuantificationFileWriter.cpp
affxparser/src/fusion_sdk/calvin_files/writers/src/CalvinCHPQuantificationFileWriter.h
affxparser/src/fusion_sdk/calvin_files/writers/src/CalvinCHPTilingFileWriter.cpp
affxparser/src/fusion_sdk/calvin_files/writers/src/CalvinCHPTilingFileWriter.h
affxparser/src/fusion_sdk/calvin_files/writers/src/CalvinCelFileWriter.cpp
affxparser/src/fusion_sdk/calvin_files/writers/src/CalvinCelFileWriter.h
affxparser/src/fusion_sdk/calvin_files/writers/src/CombinedDatConstants.h
affxparser/src/fusion_sdk/calvin_files/writers/src/CopyNumberResultWriter.cpp
affxparser/src/fusion_sdk/calvin_files/writers/src/CopyNumberResultWriter.h
affxparser/src/fusion_sdk/calvin_files/writers/src/DATFileUpdater.cpp
affxparser/src/fusion_sdk/calvin_files/writers/src/DATFileUpdater.h
affxparser/src/fusion_sdk/calvin_files/writers/src/DATFileWriter.cpp
affxparser/src/fusion_sdk/calvin_files/writers/src/DATFileWriter.h
affxparser/src/fusion_sdk/calvin_files/writers/src/DataGroupHeaderUpdater.cpp
affxparser/src/fusion_sdk/calvin_files/writers/src/DataGroupHeaderUpdater.h
affxparser/src/fusion_sdk/calvin_files/writers/src/DataGroupHeaderWriter.cpp
affxparser/src/fusion_sdk/calvin_files/writers/src/DataGroupHeaderWriter.h
affxparser/src/fusion_sdk/calvin_files/writers/src/DataGroupWriter.cpp
affxparser/src/fusion_sdk/calvin_files/writers/src/DataGroupWriter.h
affxparser/src/fusion_sdk/calvin_files/writers/src/DataSetHeaderAppend.cpp
affxparser/src/fusion_sdk/calvin_files/writers/src/DataSetHeaderAppend.h
affxparser/src/fusion_sdk/calvin_files/writers/src/DataSetHeaderUpdater.cpp
affxparser/src/fusion_sdk/calvin_files/writers/src/DataSetHeaderUpdater.h
affxparser/src/fusion_sdk/calvin_files/writers/src/DataSetHeaderWriter.cpp
affxparser/src/fusion_sdk/calvin_files/writers/src/DataSetHeaderWriter.h
affxparser/src/fusion_sdk/calvin_files/writers/src/DataSetUpdater.cpp
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affxparser/src/fusion_sdk/calvin_files/writers/src/DataSetWriter.cpp
affxparser/src/fusion_sdk/calvin_files/writers/src/DataSetWriter.h
affxparser/src/fusion_sdk/calvin_files/writers/src/FileHeaderUpdater.cpp
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affxparser/src/fusion_sdk/calvin_files/writers/src/FileHeaderWriter.cpp
affxparser/src/fusion_sdk/calvin_files/writers/src/FileHeaderWriter.h
affxparser/src/fusion_sdk/calvin_files/writers/src/FileOutput.cpp
affxparser/src/fusion_sdk/calvin_files/writers/src/FileOutput.h
affxparser/src/fusion_sdk/calvin_files/writers/src/FileWriteException.cpp
affxparser/src/fusion_sdk/calvin_files/writers/src/FileWriteException.h
affxparser/src/fusion_sdk/calvin_files/writers/src/GenericDataHeaderUpdater.cpp
affxparser/src/fusion_sdk/calvin_files/writers/src/GenericDataHeaderUpdater.h
affxparser/src/fusion_sdk/calvin_files/writers/src/GenericDataHeaderWriter.cpp
affxparser/src/fusion_sdk/calvin_files/writers/src/GenericDataHeaderWriter.h
affxparser/src/fusion_sdk/calvin_files/writers/src/GenericFileUpdater.cpp
affxparser/src/fusion_sdk/calvin_files/writers/src/GenericFileUpdater.h
affxparser/src/fusion_sdk/calvin_files/writers/src/GenericFileWriter.cpp
affxparser/src/fusion_sdk/calvin_files/writers/src/GenericFileWriter.h
affxparser/src/fusion_sdk/calvin_files/writers/src/GridControlFileWriter.cpp
affxparser/src/fusion_sdk/calvin_files/writers/src/GridControlFileWriter.h
affxparser/src/fusion_sdk/calvin_files/writers/src/MMDATFileWriter.cpp
affxparser/src/fusion_sdk/calvin_files/writers/src/MMDATFileWriter.h
affxparser/src/fusion_sdk/calvin_files/writers/src/MMDataSetDataWriter.cpp
affxparser/src/fusion_sdk/calvin_files/writers/src/MMDataSetDataWriter.h
affxparser/src/fusion_sdk/calvin_files/writers/src/MultiChannelCelFileCollater.cpp
affxparser/src/fusion_sdk/calvin_files/writers/src/MultiChannelCelFileCollater.h
affxparser/src/fusion_sdk/calvin_files/writers/src/TemplateFileWriter.cpp
affxparser/src/fusion_sdk/calvin_files/writers/src/TemplateFileWriter.h
affxparser/src/fusion_sdk/calvin_files/writers/src/TextFileWriter.cpp
affxparser/src/fusion_sdk/calvin_files/writers/src/TextFileWriter.h
affxparser/src/fusion_sdk/file
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affxparser/src/fusion_sdk/file/1LQFileData.h
affxparser/src/fusion_sdk/file/BARFileData.cpp
affxparser/src/fusion_sdk/file/BARFileData.h
affxparser/src/fusion_sdk/file/BARFileWriter.cpp
affxparser/src/fusion_sdk/file/BARFileWriter.h
affxparser/src/fusion_sdk/file/BEDFileData.cpp
affxparser/src/fusion_sdk/file/BEDFileData.h
affxparser/src/fusion_sdk/file/BEDFileWriter.cpp
affxparser/src/fusion_sdk/file/BEDFileWriter.h
affxparser/src/fusion_sdk/file/BPMAPFileData.cpp
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affxparser/src/fusion_sdk/file/BPMAPFileWriter.cpp
affxparser/src/fusion_sdk/file/BPMAPFileWriter.h
affxparser/src/fusion_sdk/file/CDFFileData.cpp
affxparser/src/fusion_sdk/file/CDFFileData.h
affxparser/src/fusion_sdk/file/CELFileData.cpp
affxparser/src/fusion_sdk/file/CELFileData.h
affxparser/src/fusion_sdk/file/CELFileWriter.cpp
affxparser/src/fusion_sdk/file/CELFileWriter.h
affxparser/src/fusion_sdk/file/CHPFileBufferWriter.cpp
affxparser/src/fusion_sdk/file/CHPFileBufferWriter.h
affxparser/src/fusion_sdk/file/CHPFileData.cpp
affxparser/src/fusion_sdk/file/CHPFileData.h
affxparser/src/fusion_sdk/file/CHPFileUpdater.cpp
affxparser/src/fusion_sdk/file/CHPFileUpdater.h
affxparser/src/fusion_sdk/file/CHPFileWriter.cpp
affxparser/src/fusion_sdk/file/CHPFileWriter.h
affxparser/src/fusion_sdk/file/CMSFileData.cpp
affxparser/src/fusion_sdk/file/CMSFileData.h
affxparser/src/fusion_sdk/file/DATFileData.cpp
affxparser/src/fusion_sdk/file/DATFileData.h
affxparser/src/fusion_sdk/file/DttArrayFileReader.cpp
affxparser/src/fusion_sdk/file/DttArrayFileReader.h
affxparser/src/fusion_sdk/file/EXPFileData.cpp
affxparser/src/fusion_sdk/file/EXPFileData.h
affxparser/src/fusion_sdk/file/FileIO.cpp
affxparser/src/fusion_sdk/file/FileIO.h
affxparser/src/fusion_sdk/file/FileWriter.cpp
affxparser/src/fusion_sdk/file/FileWriter.h
affxparser/src/fusion_sdk/file/GQCFileData.cpp
affxparser/src/fusion_sdk/file/GQCFileData.h
affxparser/src/fusion_sdk/file/GRCFileData.cpp
affxparser/src/fusion_sdk/file/GRCFileData.h
affxparser/src/fusion_sdk/file/GRCFileWriter.cpp
affxparser/src/fusion_sdk/file/GRCFileWriter.h
affxparser/src/fusion_sdk/file/GRDFileData.cpp
affxparser/src/fusion_sdk/file/GRDFileData.h
affxparser/src/fusion_sdk/file/GRDFileWriter.cpp
affxparser/src/fusion_sdk/file/GRDFileWriter.h
affxparser/src/fusion_sdk/file/GridControlData.h
affxparser/src/fusion_sdk/file/GridCoordinates.h
affxparser/src/fusion_sdk/file/IniFile.cpp
affxparser/src/fusion_sdk/file/IniFile.h
affxparser/src/fusion_sdk/file/IntervalEntry.h
affxparser/src/fusion_sdk/file/MDLFileData.cpp
affxparser/src/fusion_sdk/file/MDLFileData.h
affxparser/src/fusion_sdk/file/MSKFileData.cpp
affxparser/src/fusion_sdk/file/MSKFileData.h
affxparser/src/fusion_sdk/file/MSKFileWriter.cpp
affxparser/src/fusion_sdk/file/MSKFileWriter.h
affxparser/src/fusion_sdk/file/PSIFileData.cpp
affxparser/src/fusion_sdk/file/PSIFileData.h
affxparser/src/fusion_sdk/file/SAXDttArrayHandlers.cpp
affxparser/src/fusion_sdk/file/SAXDttArrayHandlers.h
affxparser/src/fusion_sdk/file/SMDFileData.cpp
affxparser/src/fusion_sdk/file/SMDFileData.h
affxparser/src/fusion_sdk/file/SimpleBinaryFile.cpp
affxparser/src/fusion_sdk/file/SimpleBinaryFile.h
affxparser/src/fusion_sdk/file/TagValuePair.h
affxparser/src/fusion_sdk/file/TsvFile
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affxparser/src/fusion_sdk/file/TsvFile/BgpFile.h
affxparser/src/fusion_sdk/file/TsvFile/ClfFile.cpp
affxparser/src/fusion_sdk/file/TsvFile/ClfFile.h
affxparser/src/fusion_sdk/file/TsvFile/DumpPgf.cpp
affxparser/src/fusion_sdk/file/TsvFile/DumpPgf.h
affxparser/src/fusion_sdk/file/TsvFile/PgfFile.cpp
affxparser/src/fusion_sdk/file/TsvFile/PgfFile.h
affxparser/src/fusion_sdk/file/TsvFile/SequentialClfFile.cpp
affxparser/src/fusion_sdk/file/TsvFile/SequentialClfFile.h
affxparser/src/fusion_sdk/file/TsvFile/SnpTable.cpp
affxparser/src/fusion_sdk/file/TsvFile/SnpTable.h
affxparser/src/fusion_sdk/file/TsvFile/SpfFile.cpp
affxparser/src/fusion_sdk/file/TsvFile/SpfFile.h
affxparser/src/fusion_sdk/file/TsvFile/TsvFile.cpp
affxparser/src/fusion_sdk/file/TsvFile/TsvFile.h
affxparser/src/fusion_sdk/file/TsvFile/TsvFileDiff.cpp
affxparser/src/fusion_sdk/file/TsvFile/TsvFileDiff.h
affxparser/src/fusion_sdk/file/TsvFile/TsvJoin.cpp
affxparser/src/fusion_sdk/file/TsvFile/TsvJoin.h
affxparser/src/fusion_sdk/file/TsvFile/apt-dump-pgf.cpp
affxparser/src/fusion_sdk/file/TsvFile/apt-tsv-join.cpp
affxparser/src/fusion_sdk/file/TsvFile/tsv-example.cpp
affxparser/src/fusion_sdk/file/TsvFile/tsv-test.cpp
affxparser/src/fusion_sdk/file/TsvFile/tsv-util.cpp
affxparser/src/fusion_sdk/file/test-fileio.cpp
affxparser/src/fusion_sdk/portability
affxparser/src/fusion_sdk/portability/affy-base-types.h
affxparser/src/fusion_sdk/portability/affy-system-api.h
affxparser/src/fusion_sdk/portability/apt-no-warnings.h
affxparser/src/fusion_sdk/portability/apt-win-dll.h
affxparser/src/fusion_sdk/util
affxparser/src/fusion_sdk/util/AffxArray.h
affxparser/src/fusion_sdk/util/AffxBinaryFile.cpp
affxparser/src/fusion_sdk/util/AffxBinaryFile.h
affxparser/src/fusion_sdk/util/AffxByteArray.cpp
affxparser/src/fusion_sdk/util/AffxByteArray.h
affxparser/src/fusion_sdk/util/AffxConv.cpp
affxparser/src/fusion_sdk/util/AffxConv.h
affxparser/src/fusion_sdk/util/AffxMultiDimensionalArray.h
affxparser/src/fusion_sdk/util/AffxSTL.h
affxparser/src/fusion_sdk/util/AffxSplitArray.h
affxparser/src/fusion_sdk/util/AffxStatistics.cpp
affxparser/src/fusion_sdk/util/AffxStatistics.h
affxparser/src/fusion_sdk/util/AffxString.cpp
affxparser/src/fusion_sdk/util/AffxString.h
affxparser/src/fusion_sdk/util/AffxTime.cpp
affxparser/src/fusion_sdk/util/AffxTime.h
affxparser/src/fusion_sdk/util/AptErrno.h
affxparser/src/fusion_sdk/util/AptVersionInfo.h
affxparser/src/fusion_sdk/util/BaseEngine.cpp
affxparser/src/fusion_sdk/util/BaseEngine.h
affxparser/src/fusion_sdk/util/CalvinChpCheck.h
affxparser/src/fusion_sdk/util/CalvinToText.cpp
affxparser/src/fusion_sdk/util/CalvinToText.h
affxparser/src/fusion_sdk/util/CelCheck.h
affxparser/src/fusion_sdk/util/ChpCheck.h
affxparser/src/fusion_sdk/util/Convert.cpp
affxparser/src/fusion_sdk/util/Convert.h
affxparser/src/fusion_sdk/util/DotProgress.cpp
affxparser/src/fusion_sdk/util/DotProgress.h
affxparser/src/fusion_sdk/util/Engines.h
affxparser/src/fusion_sdk/util/Err.cpp
affxparser/src/fusion_sdk/util/Err.h
affxparser/src/fusion_sdk/util/ErrHandler.h
affxparser/src/fusion_sdk/util/Except.h
affxparser/src/fusion_sdk/util/FrugalVector.h
affxparser/src/fusion_sdk/util/Fs.cpp
affxparser/src/fusion_sdk/util/Fs.h
affxparser/src/fusion_sdk/util/FsPath.cpp
affxparser/src/fusion_sdk/util/FsPath.h
affxparser/src/fusion_sdk/util/Guid.cpp
affxparser/src/fusion_sdk/util/Guid.h
affxparser/src/fusion_sdk/util/LineFile.cpp
affxparser/src/fusion_sdk/util/LineFile.h
affxparser/src/fusion_sdk/util/LogStream.cpp
affxparser/src/fusion_sdk/util/LogStream.h
affxparser/src/fusion_sdk/util/MatrixCheck.h
affxparser/src/fusion_sdk/util/MessageStream.h
affxparser/src/fusion_sdk/util/MixedFileCheck.h
affxparser/src/fusion_sdk/util/MsgHandler.h
affxparser/src/fusion_sdk/util/MsgSocketHandler.cpp
affxparser/src/fusion_sdk/util/MsgSocketHandler.h
affxparser/src/fusion_sdk/util/MsgStream.cpp
affxparser/src/fusion_sdk/util/MsgStream.h
affxparser/src/fusion_sdk/util/Options.cpp
affxparser/src/fusion_sdk/util/Options.h
affxparser/src/fusion_sdk/util/OutputMessageStream.cpp
affxparser/src/fusion_sdk/util/OutputMessageStream.h
affxparser/src/fusion_sdk/util/PgOptions.cpp
affxparser/src/fusion_sdk/util/PgOptions.h
affxparser/src/fusion_sdk/util/Progress.h
affxparser/src/fusion_sdk/util/ProgressDot.h
affxparser/src/fusion_sdk/util/ProgressHandler.h
affxparser/src/fusion_sdk/util/RowFile.cpp
affxparser/src/fusion_sdk/util/RowFile.h
affxparser/src/fusion_sdk/util/SQLite.cpp
affxparser/src/fusion_sdk/util/SQLite.h
affxparser/src/fusion_sdk/util/SocketBase.cpp
affxparser/src/fusion_sdk/util/SocketBase.h
affxparser/src/fusion_sdk/util/SocketClient.cpp
affxparser/src/fusion_sdk/util/SocketClient.h
affxparser/src/fusion_sdk/util/SocketEngine.cpp
affxparser/src/fusion_sdk/util/SocketEngine.h
affxparser/src/fusion_sdk/util/SocketHandler.cpp
affxparser/src/fusion_sdk/util/SocketHandler.h
affxparser/src/fusion_sdk/util/SocketServer.cpp
affxparser/src/fusion_sdk/util/SocketServer.h
affxparser/src/fusion_sdk/util/SocketTextHandler.cpp
affxparser/src/fusion_sdk/util/SocketTextHandler.h
affxparser/src/fusion_sdk/util/SocketUtil.cpp
affxparser/src/fusion_sdk/util/SocketUtil.h
affxparser/src/fusion_sdk/util/TableFile.cpp
affxparser/src/fusion_sdk/util/TableFile.h
affxparser/src/fusion_sdk/util/TextFileCheck.h
affxparser/src/fusion_sdk/util/TmpFileFactory.cpp
affxparser/src/fusion_sdk/util/TmpFileFactory.h
affxparser/src/fusion_sdk/util/Util.cpp
affxparser/src/fusion_sdk/util/Util.h
affxparser/src/fusion_sdk/util/Verbose.cpp
affxparser/src/fusion_sdk/util/Verbose.h
affxparser/src/fusion_sdk/util/VerboseErrHandler.h
affxparser/src/fusion_sdk/util/apt-check-calvinchp.cpp
affxparser/src/fusion_sdk/util/apt-check-cel.cpp
affxparser/src/fusion_sdk/util/apt-check-chp.cpp
affxparser/src/fusion_sdk/util/apt-check-matrix.cpp
affxparser/src/fusion_sdk/util/apt-check-mixedfile.cpp
affxparser/src/fusion_sdk/util/apt-check-textfile.cpp
affxparser/src/fusion_sdk/util/apt-engine-wrapper.cpp
affxparser/src/fusion_sdk/util/apt-engine-wrapper.vcproj
affxparser/src/fusion_sdk/util/chksum.cpp
affxparser/src/fusion_sdk/util/chksum.h
affxparser/src/fusion_sdk/util/dump-guid.cpp
affxparser/src/fusion_sdk/util/md5.cpp
affxparser/src/fusion_sdk/util/md5.h
affxparser/src/fusion_sdk/util/md5sum.cpp
affxparser/src/fusion_sdk/util/md5sum.h
affxparser/src/fusion_sdk/util/test-md5sum.cpp
affxparser/src/fusion_sdk/util/test-tmpfilefactory.cpp
affxparser/src/fusion_sdk/util/util-meminfo.cpp
affxparser/tests
affxparser/tests/convertCel.R
affxparser/tests/readCdfDataFrame.R
affxparser/tests/readCdfQc.R
affxparser/tests/readCdfUnitsWriteMap.R
affxparser/tests/readCdfUnits_etal.R
affxparser/tests/readCel.R
affxparser/tests/readCelIntensities.R
affxparser/tests/readCelRectangle.R
affxparser/tests/readCelUnits.R
affxparser/tests/readPgf.R
affxparser/tests/testWriteAndReadEmptyCdf.R
affxparser/tests/testWriteAndReadEmptyCel.R
affxparser/tests/torture
affxparser/tests/torture/tortureReadCdfUnits.R
affxparser/tests/torture/tortureReadCel.R
affxparser/tests/torture/tortureReadCelHeader.R
affxparser/tests/torture/tortureReadCelUnits.R
affxparser/tests/validate
affxparser/tests/validate/validateCelFileFormats.R

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