#/*****************************************************************************
##   Copyright (C) 1994-2008 by David Gordon.
##   All rights reserved.                           
##                                                                           
##   This software is part of a beta-test version of the Consed/Autofinish
##   package.  It should not be redistributed or
##   used for any commercial purpose, including commercially funded
##   sequencing, without written permission from the author and the
##   University of Washington.
##   
##   This software is provided ``AS IS'' and any express or implied
##   warranties, including, but not limited to, the implied warranties of
##   merchantability and fitness for a particular purpose, are disclaimed.
##   In no event shall the authors or the University of Washington be
##   liable for any direct, indirect, incidental, special, exemplary, or
##   consequential damages (including, but not limited to, procurement of
##   substitute goods or services; loss of use, data, or profits; or
##   business interruption) however caused and on any theory of liability,
##   whether in contract, strict liability, or tort (including negligence
##   or otherwise) arising in any way out of the use of this software, even
##   if advised of the possibility of such damage.
##
##   Building Consed from source is error prone and not simple which is
##   why I provide executables.  Due to time limitations I cannot
##   provide any assistance in building Consed.  Even if you do not
##   modify the source, you may introduce errors due to using a
##   different version of the compiler, a different version of motif,
##   different versions of other libraries than I used, etc.  For this
##   reason, if you discover Consed bugs, I can only offer help with
##   those bugs if you first reproduce those bugs with an executable
##   provided by me--not an executable you have built.
## 
##   Modifying Consed is also difficult.  Although Consed is modular,
##   some modules are used by many other modules.  Thus making a change
##   in one place can have unforeseen effects on many other features.
##   It may takes months for you to notice these other side-effects
##   which may not seen connected at all.  It is not feasable for me to
##   provide help with modifying Consed sources because of the
##   potentially huge amount of time involved.
##
##*****************************************************************************/
#!/bin/sh


dgetcopy \
\
\
abs.h \
addAlignedSequence.cpp \
addAlignedSequence.h \
addNewReads.cpp \
addNewReads.h \
addNewReadsAutomated.cpp \
addNewReadsAutomated.h \
addNewReadsWithExistingAlignments.cpp \
addNewReadsWithExistingAlignments.h \
addTearTagType.cpp \
addTearTagType.h \
alignmentPiece.h \
applyEditHistory.cpp \
applyEditHistory.h \
arrayOfFwdRevPairLines.cpp \
arrayOfFwdRevPairLines.h \
arrayOfFwdRevPairSquares.cpp \
arrayOfFwdRevPairSquares.h \
arrayOfFwdRevPairTriangles.cpp \
arrayOfFwdRevPairTriangles.h \
arrayOfRestrictionFragments.h \
assembly.cpp \
assembly.h \
assembly2.cpp \
assembly3.cpp \
assembly4.cpp \
assembly5.cpp \
assemblyView.cpp \
assemblyView2.cpp \
assemblyView3.cpp \
assemblyView4.cpp \
assemblyView.h \
assemblyViewRemoveReads.cpp \
assemblyViewRemoveReads.h \
assemblyViewTagTypeAndLine.h \
assert.cpp \
assert.h \
assignDistributions.h \
autoEdit.cpp \
autoEdit.h \
autoFinish.cpp \
autoFinish.h \
autoFinishExpTag.cpp \
autoFinishExpTag.h \
autoFinishPCR.cpp \
autoFinishPCR.h \
autoFinishPurposes.h \
autoReport.cpp \
autoReport.h \
automatedConsedInit.cpp \
automatedConsedInit.h \
autoPCRAmplify.cpp \
autoPCRAmplify.h \
bAllNeededSpecies.h \
bDoPCRPrimersStickToEachOther.cpp \
bDoPCRPrimersStickToEachOther.h \
bEditHistoryFileExists.cpp \
bEditHistoryFileExists.h \
bErrorMessageIfNoPhd.cpp \
bErrorMessageIfNoPhd.h \
bForwardReversePairIsConsistentWithContigOrder.cpp \
bForwardReversePairIsConsistentWithContigOrder.h \
bGuiGetAnswerYesNo.cpp \
bGuiGetAnswerYesNo.h \
bInputEventToWrongWindow.cpp \
bInputEventToWrongWindow.h \
bIntersect.h \
bIntersectLong.h \
bIntervalsIntersect.h \
bIntervalsIntersectLong.h \
bIsABase.h \
bIsAPad.h \
bNotACGTTable.h \
basesAndQualitiesAndPeaks.cpp \
basesAndQualitiesAndPeaks.h \
batchChangeConsensus.cpp \
batchChangeConsensus.h \
breakIntoShorterLines.cpp \
breakIntoShorterLines.h


dgetcopy \
\
\
bIsDyePrimerNotDyeTerminator.h \
bIsNumeric.cpp \
bIsNumeric.h \
bIsNumericDouble.cpp \
bIsNumericDouble.h \
bIsNumericFloat.cpp \
bIsNumericFloat.h \
bIsNumericLongMaybeWithWhitespace.cpp \
bIsNumericLongMaybeWithWhitespace.h \
bIsNumericMaybeWithWhitespace.cpp \
bIsNumericMaybeWithWhitespace.h \
bIsPCRPrimerPairOK.cpp \
bIsPCRPrimerPairOK.h \
bIsPrimerStale.cpp \
bIsPrimerStale.h \
bIsStartCodon.h \
bIsStopCodon.h \
bIsTopStrandRead.cpp \
bIsTopStrandRead.h \
bPrimerHasMatchesAgainstSequencesInFile.cpp \
bPrimerHasMatchesAgainstSequencesInFile.h \
bPrimerHasMatchesElsewhere.cpp \
bPrimerHasMatchesElsewhere.h \
baseSegmentsToSort.h \
basesegment.cpp \
basesegment.h \
bigArrayOfLittleArraysOfDistributions.cpp \
bigArrayOfLittleArraysOfDistributions.h \
blockOfLocationsOfA4MerType.h \
bool.h \
busy_cursor.cpp \
busy_cursor.h \
cComplementBase.h \
cComplementBaseTable.h \
cGetProtein.cpp \
cGetProtein.h \
calculatePrimerMeltingTemperatures.cpp \
calculatePrimerMeltingTemperatures.h \
centerWidgetOnWidget.cpp \
centerWidgetOnWidget.h \
checkPrimersForACGT.cpp \
checkPrimersForACGT.h \
checkLicenseKey.cpp \
checkLicenseKey.h \
checkLicenseKeyStub.cpp \
checkPrimersForMononucleotideRepeats.cpp \
checkPrimersForMononucleotideRepeats.h \
checkVariableLengthLimit.cpp.part1 \
checkVariableLengthLimit.cpp.part3 \
checkVariableLengthLimit.h \
choose_contig.cpp \
choose_contig.h \
chromatData.c \
chromatData.h \
clScaffold.cpp \
clScaffold.h \
collectableLocatedFragmentPtr.h \
colorDefaults.cpp \
colorDefaults.h.part1 \
colorDefaults.h.part3 \
colormode.cpp \
colormode.h \
compareContigs.cpp \
compareContigs.h \
compareContigs2.cpp \
compareContigsCursor.h \
compareContigsTypes.h \
compareOnePrimerAndOneSequence.cpp \
compareOnePrimerAndOneSequence.h \
complementSequence.cpp \
complementSequence.h \
complement_so.cpp \
complement_so.h \
consed.cpp \
consed.h \
consedParameters.cpp.part1 \
consedParameters.cpp.part3 \
consedParameters.h.part1 \
consedParameters.h.part3 \
consedParameters3.cpp \
consedResources.cpp.part1 \
consedResources.cpp.part3 \
consedResources.h.part1 \
consedResources.h.part3 \
consedResources.txt \
consedResources2.cpp.part1 \
consedResources2.cpp.part3 \
consedResources3.cpp.part1 \
consedResources3.cpp.part3 \
consed_version.h \
contig.cpp \
contig.h \
contig2.cpp \
contig4.cpp \
contig5.cpp \
contig6.cpp \
contig7.cpp \
contig8.cpp \
contig9.cpp \
contig10.cpp \
contig11.cpp \
contig12.cpp \
contigEnd.h \
contigEndPair.cpp \
contigEndPair.h \
contigEndReadList.cpp \
contigEndReadList.h \
contigMatchTablesType.h \
contigSegment.h \
contigview.cpp \
contigview.h \
contigwin.cpp \
contigwin.h \
copyFiles.cpp \
copyFiles.h \
copyPrimerMatchesFromShorterToLongerPrimers.cpp \
copyPrimerMatchesFromShorterToLongerPrimers.h \
correspondingFragments.h \
countsOfWhyPrimersAreNotAcceptable.cpp \
countsOfWhyPrimersAreNotAcceptable.h \
createPrimerCandidate.cpp \
createPrimerCandidate.h \
createPrimerCandidates.cpp \
createPrimerCandidates.h \
createPrimerCandidatesWith3PrimeEnd.cpp \
createPrimerCandidatesWith3PrimeEnd.h \
createTearTags.cpp \
createTearTags.h \
createUnalignedHighQualityNavigator.cpp \
createUnalignedHighQualityNavigator.h \
crossMatchInfoForRead.cpp \
crossMatchInfoForRead.h \
crossMatchIndel.h \
customNavigation.cpp \
customNavigation.h \
dErrorRateFromQuality.h \
dGetErrorsFixedAtBase.h \
dGetPrimerMeltingTemperature.cpp \
dGetPrimerMeltingTemperature.h \
decisionbox.cpp \
decisionbox.h \
defaultResources.h \
defaultResourcesDefinition.h.part1 \
defaultResourcesDefinition.h.part3 \
deleteFileIfItExists.cpp \
deleteFileIfItExists.h \
deleteFileOrPopupErrorMessage.cpp \
deleteFileOrPopupErrorMessage.h \
dictionary.cpp \
dictionary.h \
diffChromosomes.cpp \
diffChromosomes.h \
digestForOneEnzyme.cpp \
digestForOneEnzyme.h \
displayPrimers.cpp \
displayPrimers.h \
distribution.cpp \
distribution.h \
dumpCore.cpp \
dumpCore.h \
dumpDistribution.h \
editActionChangeRead.h \
editAddConsensusTag.cpp \
editAddConsensusTag.h \
editAddReadTag.cpp \
editAddReadTag.h \
editAddTagsToAllReadsAtConsPos.cpp \
editAddTagsToAllReadsAtConsPos.h \
editChangeToNs.h \
editChangeToNsToLeft.h \
editChangeToNsToRight.h \
editChangeToXs.h \
editCursor.cpp \
editCursor.h \
editDeleteConsensusTag.cpp \
editDeleteConsensusTag.h \
editDeleteReadTag.cpp \
editDeleteReadTag.h \
editInsertColOfPads.cpp \
editInsertColOfPads.h \
editMakeHighQuality.h \
editMakeHighQualityAndChangeConsensus.cpp \
editMakeHighQualityAndChangeConsensus.h \
editMakeLowQuality.h \
editMakeLowQualityToLeft.h \
editMakeLowQualityToRight.h \
editOverstrike.h \
editOverstrikeAllReadsAtConsPos.cpp \
editOverstrikeAllReadsAtConsPos.h \
editOverstrikeConsensus.cpp \
editOverstrikeConsensus.h \
edit_complement_contig.cpp \
edit_complement_contig.h \
editaction.cpp \
editaction.h \
editedButNotNsGotoList.cpp \
editedButNotNsGotoList.h \
editedGotoList.cpp \
editedGotoList.h \
evalExpCluster.cpp \
evalExpCluster.h \
exclusive_or.h \
experiment.cpp \
experiment.h \
expidAndLocatedFragment.h \
extendAlignment.cpp \
extendAlignment.h \
extendAlignmentBanded.cpp \
extendAlignmentBanded.h \
fallbackConsedResources.h.part1 \
fallbackConsedResources.h.part3 \
fGetDistanceFromPointToLine.h \
fGetDistanceFromPointToPoint.h \
fileDefines.h \
filePopupAndGetAceFilename.cpp \
filePopupAndGetAceFilename.h \
filePopupAndGetFilename.cpp \
filePopupAndGetFilename.h \
filename.cpp \
filename.h \
filenamePlus.h \
fileselector.cpp \
fileselector.h \
filFindSolexaPrbFileFromSeqFile.cpp \
filFindSolexaPrbFileFromSeqFile.h \
filGetUniqueFilename.cpp \
filGetUniqueFilename.h \
findAncestralTrees.cpp \
findAncestralTrees.h \
findPrimerMatchesAgainstSequencesInFile.cpp \
findPrimerMatchesAgainstSequencesInFile.h \
findPrimerMatchesElsewhere.cpp \
findPrimerMatchesElsewhere.h \
findPrimerSelfMatches.cpp \
findPrimerSelfMatches.h \
findQueryWithinSubject.cpp \
findQueryWithinSubject.h \
findRepeat.cpp \
findRepeat.h \
findStickiestSelfMatch.cpp \
findStickiestSelfMatch.h \
findTemplatesForPrimers.cpp \
findTemplatesForPrimers.h \
findTraceExtrema.c \
findTraceExtrema.h \
fixContigEnd.cpp \
fixContigEnd.h \
fixContigEnds.cpp \
fixContigEnds.h \
fragment_and_contig.cpp \
fragment_and_contig.h \
freeChromatData.h \
fullSmithWaterman.cpp \
fullSmithWaterman.h \
fwdRevPair.h \
fwdRevPair2.h \
fwdRevPairLine.cpp \
fwdRevPairLine.h \
fwdRevPairSquare.cpp \
fwdRevPairSquare.h \
fwdRevPairTriangle.cpp \
fwdRevPairTriangle.h \
geneClassifications.cpp \
geneClassifications.h \
getAlignment.cpp \
getAlignment.h \
getAlignmentBanded.cpp \
getAlignmentBanded.h \
getAllSinglets.cpp \
getAllSinglets.h \
getAllTokens.cpp \
getAllTokens.h \
getNextToken.cpp \
getNextToken.h \
gotoList.cpp


dgetcopy \
\
\
gotoList.h \
gotoListType.h \
groupOfPrimers.h \
guiAddNewReads.cpp \
guiAddNewReads.h \
guiAskUserToSelectReadListOptions.cpp \
guiAskUserToSelectReadListOptions.h \
guiAssemblyViewIncludeContigs.cpp \
guiAssemblyViewIncludeContigs.h \
guiAssemblyViewReadDepth.cpp \
guiAssemblyViewReadDepth.h \
guiAssemblyViewShowTags.cpp \
guiAssemblyViewShowTags.h \
guiAssemblyViewWhatToShow.cpp \
guiAssemblyViewWhatToShow.h \
guiChangeColor.cpp \
guiChangeColor.h \
guiCheckPrimer.cpp \
guiCheckPrimer.h \
guiChoiceOfReadsForAlignedReads.cpp \
guiChoiceOfReadsForAlignedReads.h \
guiChoiceOfSeqMatches.cpp \
guiChoiceOfSeqMatches.h \
guiCompareContigs.cpp \
guiCompareContigs.h \
guiDigestProblemNavigator.cpp \
guiDigestProblemNavigator.h \
guiDisplayDigest.cpp \
guiDisplayDigest.h \
guiEditResources.cpp.part1 \
guiEditResources.cpp.part3 \
guiEditResources.cpp.part5 \
guiEditResources.cpp.part7 \
guiEditResources.cpp.part9 \
guiEditResources.cpp.part11 \
guiEditResources.h.part1 \
guiEditResources.h.part3 \
guiEditResources.h.part5 \
guiEditResourcesStandalone.cpp \
guiEditResourcesStandalone.h \
guiExportConsensusWithOptions.cpp \
guiExportConsensusWithOptions.h \
guiFindRestrictionEnzymeSites.cpp \
guiFindRestrictionEnzymeSites.h \
guiGetCommentForTag.cpp \
guiGetCommentForTag.h \
guiGetReferenceRead.cpp \
guiGetReferenceRead.h \
guiGetTagType.cpp \
guiGetTagType.h \
guiGetUserDefinedTagInfo.cpp \
guiGetUserDefinedTagInfo.h \
guiHowToSortAlignedReads.cpp \
guiHowToSortAlignedReads.h \
guiMultiContigNavigator.cpp \
guiMultiContigNavigator.h \
guiNavigateByHighlyDiscrepantPositions.cpp \
guiNavigateByHighlyDiscrepantPositions.h \
guiNavigateByReadDepth.cpp \
guiNavigateByReadDepth.h \
guiPopupDocumentation.cpp \
guiPopupDocumentation.h \
guiPopupTagInfo.cpp \
guiPopupTagInfo.h \
guiPopupWholeReadItem.cpp \
guiPopupWholeReadItem.h \
guiQuit.cpp \
guiQuit.h \
guiQuitTypes.h \
guiRemoveReads.cpp \
guiRemoveReads.h \
guiReorderContigs.cpp \
guiReorderContigs.h \
guiReorientContigs.cpp \
guiReorientContigs.h \
guiSaveHighlightedReads.cpp \
guiSaveHighlightedReads.h \
guiSearchForOligoTags.cpp \
guiSearchForOligoTags.h \
guiSearchForOpenReadingFrames.cpp \
guiSearchForOpenReadingFrames.h \
guiSearchForTagsByComment.cpp \
guiSearchForTagsByComment.h \
guiSetGeneralPreferences.cpp \
guiSetGeneralPreferences.h \
guiSetPrimerPickingPreferences.cpp \
guiSetPrimerPickingPreferences.h \
guiShowErrorInfoForARegion.cpp \
guiShowErrorInfoForARegion.h \
guiTearContig.cpp \
guiTearContig.h \
guiTopWindow.cpp \
guiTopWindow.h \
guiTriangle.h \
guiUndoEdit.cpp \
guiUndoEdit.h \
guiWhatToDoWithSelection.cpp \
guiWhatToDoWithSelection.h \
gui_get_selection.cpp \
gui_get_selection.h \
gui_search_for_string.cpp \
gui_search_for_string.h \
guiapp.cpp \
guiapp.h \
guicolortext.cpp \
guicolortext.h \
guicontigwin.cpp \
guicontigwin.h \
guidraw.cpp \
guieditwin.cpp \
guieditwin.h \
guihighlight.cpp \
guihighlight.h \
guiinput.cpp \
guiresize.cpp \
guiteditor.cpp \
guiteditor.h \
guitedwin.cpp \
guitedwin.h \
handleWindowManagerDelete.cpp \
handleWindowManagerDelete.h \
handleWindowManagerDelete2.cpp \
handleWindowManagerDelete2.h \
hideSomeTagTypes.cpp \
hideSomeTagTypes.h \
highQualityDiscrepancyGotoList.cpp \
highQualityDiscrepancyGotoList.h \
hp_exception_kludge.h \
infobutton.cpp \
infobutton.h \
intXtPointerUnion.h \
kimuraBranchProb.cpp \
kimuraBranchProb.h \
library.cpp \
library.h \
listOfFragments.h \
listOfFragmentsAndEndPositions.h \
listOfLibraries.cpp \
listOfLibraries.h \
locatedFragment.cpp \
locatedFragment.h \
lookForFalsePrimerMatchesOfOnePrimerInOneContig.cpp \
lookForFalsePrimerMatchesOfOnePrimerInOneContig.h \
lookForImperfect3Prime4MerFalsePrimerMatchesOfOnePrimerInOneContig.cpp \
lookForImperfect3Prime4MerFalsePrimerMatchesOfOnePrimerInOneContig.h \
lookForPerfect4MerFalsePrimerMatchesOfOnePrimerInOneContig.cpp \
lookForPerfect4MerFalsePrimerMatchesOfOnePrimerInOneContig.h \
lowconsqual.cpp \
lowconsqual.h \
main.cpp_part1 \
main.cpp_part5 \
main.cpp_part6b \
main.cpp_part8 \
main.cpp_part11 \
makeDependMelakwa.perl \
makeDistributionAllOnes.h \
makeMainCPP.perl \
makeMainCPP.txt \
makeNewG++.perl \
makeOldG++.perl \
makeUpper.c \
makeUpper.h \
makeVectorLookupTables.cpp \
makeVectorLookupTables.h \
matchLinker.h \
matchScores.h \
matchWithinAssembly.h \
max.h \
maybeTerminateIfAnotherReadWriteConsed.cpp \
maybeTerminateIfAnotherReadWriteConsed.h \
mbtPtrOrderedVector.h \
mbtPtrVector.h \
mbtValOrderedVectorOfInt.cpp \
mbtValOrderedVectorOfInt.h \
mbtValOrderedVectorOfLong.h \
mbtValOrderedVectorOfRWCString.h \
mbtValVector.cpp \
mbtValVector.h \
mbtValVectorOfBool.h \
mbtValVector_inc.cpp \
mbt_errors.h \
mbt_exception.cpp \
mbt_exception.h \
mbt_val_ord_offset_vec.h \
messageAndFileSelector.cpp \
messageAndFileSelector.h \
min.h \
miniassembly.cpp \
miniassembly.h \
miscProgram.cpp \
miscProgram.h \
mk_header_chinook \
mk_header_enki \
mk_header_kwakiutl \
mk_header_kwakiutl_dyn \
mk_header_kwakiutl_gprof \
mk_header_kwakiutl_opt \
mk_header_melakwa \
mk_header_melakwa_dyn \
mk_header_melakwa_for_make_dependencies \
mk_header_tillamook \
mk_header_tlingit \
mk_header_umpqua \
mk_header_walrus \
mk_header_wherry_dyn \
mk_header_wherry \
mk_header_widget \
mk_header_winter \
mk_header_wit \
mk_header_wit_dyn \
mk_kwakiutl_guiEditResources \
mk_targets \
motifutils.cpp \
motifutils.h \
multiProblemGotoList.cpp \
multiProblemGotoList.h \
multiplyDistributionWithMinimum.h \
multiplyDistributions.h \
multiplyDistributions2.h \
multiplyDistributions3.h \
myAgrep.cpp \
myAgrep.h \
myAgrepAndFilter.cpp \
myAgrepAndFilter.h \
nAmbiguityCodeToNumber2.cpp \
nAmbiguityCodeToNumber2.h \
nCompareContigsByName.cpp \
nCompareContigsByName.h \
nConvertFrom4Mer.h \
nCountPadsAndConvertFormat.h \
nCreateSocket.cpp \
nCreateSocket.h \
nDeleteFile.cpp \
nDeleteFile.h \
nFindScoreOfMatch.cpp \
nFindScoreOfMatch.h \
nFindScoreOfSelfMatch.cpp \
nFindScoreOfSelfMatch.h \
nGetAmountOfOverlap.h \
nGetLengthOfMononucleotideRepeat.cpp \
nGetLengthOfMononucleotideRepeat.h \
nGetNumberOfTokens.cpp \
nGetNumberOfTokens.h \
nGetReadTypeFromReadName.cpp \
nGetReadTypeFromReadName.h \
nGetTrailingNumber.cpp \
nGetTrailingNumber.h \
nLengthOf4Mer.h \
nLine.h \
nMAX_QUALITY_LEVEL2.h \
nNumberFromBase.h \
nNumberFromBase2.h \
nNumberFromBase3.h \
nNumberFromBase4.h \
nPrimerFalseMatchScoreArray.h \
nStripTrailingWhitespace.cpp \
nStripTrailingWhitespace.h \
nSystemReadALine.cpp \
nSystemReadALine.h \
navigateByTagsInAllContigs.cpp \
navigateByTagsInAllContigs.h \
newContig.h \
nextPhredPipeline.cpp \
nextPhredPipeline.h \
ntide.cpp \
ntide.h \
numutil.cpp \
numutil.h \
oligoTag.cpp \
oligoTag.h \
openAutoFinishOutputFiles.cpp \
openAutoFinishOutputFiles.h \
openLogFiles.cpp \
openLogFiles.h \
ostream_overloads.cpp \
ourFree.h \
ourMalloc.h \
pFindShortestAcceptablePrimer.cpp \
pFindShortestAcceptablePrimer.h \
paddedFromUnpadded.cpp \
paddedFromUnpadded.h \
paddedPieceOfRead.cpp \
paddedPieceOfRead.h \
paddedPieceOfSequence.cpp \
paddedPieceOfSequence.h \
parseAceFile.cpp \
parseAceFile.h \
parseConsedResources.perl \
parseUserDefinedTagTypeLine.cpp \
parseUserDefinedTagTypeLine.h \
pcrPrimer.cpp \
pcrPrimer.h \
pcrPrimerPair.h \
pcrPrimerPairSubscripts.h \
pcrPrimerrPair.cpp \
pcrPrimerrPair.h \
perhapsCreateSocketToControlConsed.cpp \
perhapsCreateSocketToControlConsed.h

dgetcopy \
\
\
phaster2PhdBall.cpp \
phaster2PhdBall.h \
phdBall2Fasta.cpp \
phdBall2Fasta.h \
phredUtilities.c \
pickCombinationsOfPCRPrimers.cpp \
pickCombinationsOfPCRPrimers.h \
pickPCRPrimers.cpp \
pickPCRPrimers.h \
pickPCRPrimersForOneEndOfContig.cpp \
pickPCRPrimersForOneEndOfContig.h \
pickPrimers.cpp \
pickPrimers.h \
please_wait.cpp \
please_wait.h \
popupErrorMessage.cpp \
popupErrorMessage.h \
popupErrorMessage2.cpp \
popupErrorMessage2.h \
popupInfoMessage.cpp \
popupInfoMessage.h \
popupInfoOrErrorMessageNoFormat.cpp \
popupInfoOrErrorMessageNoFormat.h \
primateSpecies.cpp \
primateSpecies.h \
primerStickiestFalseMatch.cpp \
primerStickiestFalseMatch.h \
primerType.h \
printAlignment.cpp \
printAlignment.h \
printAutoFinishMiscInfo.cpp \
printAutoFinishMiscInfo.h \
printAutoFinishParameters.cpp.part1 \
printAutoFinishParameters.cpp.part3 \
printAutoFinishParameters.h \
printChangedAutoFinishParameters.cpp.part1 \
printChangedAutoFinishParameters.cpp.part3 \
printChangedAutoFinishParameters.h \
printDefaultResources.cpp \
printDefaultResources.h \
printMemory.cpp \
printMemory.h \
printPS.cpp \
printPS.h \
printSingleSignal.cpp \
printSingleSignal.h \
printTime.cpp \
printTime.h \
procToRunWhenSomeOtherProgramConnectsToConsed.cpp \
procToRunWhenSomeOtherProgramConnectsToConsed.h \
processReadme.perl \
quality.h \
readABI.c \
readABI.h \
readAndProcessReadPrefixFile.cpp \
readAndProcessReadPrefixFile.h \
readData.c \
readData.h \
readESD.c \
readESD.h \
readFileOfPhdFiles.cpp \
readFileOfPhdFiles.h \
README.txt \
readOneSffFile.cpp \
readOneSffFile.h \
readPHD.cpp \
readPHD.h \
readPHDAgainForHighQualitySegment.cpp \
readPHDAgainForHighQualitySegment.h \
readPHDOfSinglet.cpp \
readPHDOfSinglet.h \
readPrimerScreenSequences.cpp \
readPrimerScreenSequences.h \
readSCF.c \
readSCF.h \
readSCF2.c \
readSCF3.c \
readSCFUtil.c \
readType.c \
readType.h \
readTypes.h \
readWholeReadItem.cpp \
readWholeReadItem.h \
readsSortedByLeftEndPosition.h \
readsSortedByReadName.h \
readsSortedByTemplateName.h \
readsense_bitmaps.h \
regionOfContig.h \
regionOfSequence.h \
regionOfSequenceArray.cpp \
regionOfSequenceArray.h \
regionToAmplify.cpp \
regionToAmplify.h \
removeContigs.cpp \
removeContigs.h \
removeReads.cpp \
removeReads.h \
renameFiles.cpp \
renameFiles.h \
restrictionEnzyme.h \
restrictionEnzymes.h \
restrictionFragment.cpp \
restrictionFragment.h \
restrictionFragmentMobility.h \
rwUtil.c \
rwUtil.h \
rwbtreedictionary.h \
rwcregexp.cpp \
rwcregexp.h \
rwcstring.cpp \
rwcstring.h \
rwcsubstring.cpp \
rwcsubstring.h \
rwctokenizer.cpp \
rwctokenizer.h \
rwdefs.h \
rwt2dptrvector.h \
rwt2dvalvector.h \
rwtptrorderedvector.cpp \
rwtptrorderedvector.h \
rwtptrorderedvector_inc.cpp \
rwtptrsortedvector.cpp \
rwtptrsortedvector.h \
rwtptrvector.h \
rwtvalorderedvector.cpp \
rwtvalorderedvector.h \
rwtvalorderedvector_inc.cpp \
rwtvalsortedvector.h \
rwtvalvector.h

dgetcopy \
\
\
saveTagTypes.cpp.part1 \
saveTagTypes.cpp.part3 \
saveTagTypes.h \
saveTagTypesFromFile.cpp \
saveTagTypesFromFile.h \
scaleTickSizes.h \
searchForSingleStrandedRegions.cpp \
searchForSingleStrandedRegions.h \
searchForSingleSubcloneRegions.cpp \
searchForSingleSubcloneRegions.h \
searchMethods.h \
search_for_string.cpp \
search_for_string.h \
selection.cpp \
selection.h \
seqJustBases.h \
seqMatch.cpp \
seqMatch.h \
sequence.cpp \
sequence.h \
setComplementBaseTable.cpp \
setComplementBaseTable.h \
setErrorRateFromQuality.cpp \
setErrorRateFromQuality.h \
setMatchLookupTable.cpp \
setMatchLookupTable.h \
setMatchMatrix.cpp \
setMatchMatrix.h \
setNotACGTTable.cpp \
setNotACGTTable.h \
setNumberFromBase4.cpp \
setNumberFromBaseTable.cpp \
setNumberFromBaseTable.h \
setPrimerFalseMatchScoreArray.cpp \
setPrimerFalseMatchScoreArray.h \
sff2PhdBall.cpp \
sff2PhdBall.h \
singleStrandedRegionsGotoList.cpp \
singleStrandedRegionsGotoList.h \
singleSubcloneRegionsGotoList.cpp \
singleSubcloneRegionsGotoList.h \
singletInfo.h \
singletsSortedByTemplateName.h \
snpGenome.cpp \
snpGenome.h \
soAddCommas.cpp \
soAddCommas.h \
soEmptyString.h \
soFindFlowCellFromPath.cpp \
soFindFlowCellFromPath.h \
soGetBranchNameWithoutTree.h \
soGetChemistry.cpp \
soGetChemistry.h \
soGetDate.cpp \
soGetDate.h \
soGetDateTime.cpp \
soGetDateTime.h \
soDecodePhasterBasesToGenomic.cpp \
soDecodePhasterBasesToGenomic.h \
soDecodePhasterBasesToRead.cpp \
soDecodePhasterBasesToRead.h \
soGetErrno.cpp \
soGetErrno.h \
soGetRequiredBases.cpp \
soGetRequiredBases.h \
soGetRestOfLine.cpp \
soGetRestOfLine.h \
soLine.h \
socketConnection.h \
solexa2PhdBall.cpp \
solexa2PhdBall.h \
someOtherProgramSentACommandToConsed.cpp \
someOtherProgramSentACommandToConsed.h \
sortAcceptablePrimers.cpp \
sortAcceptablePrimers.h \
sortPrimersByEndPosition.cpp \
sortPrimersByEndPosition.h \
sortPrimersByStartPosition.cpp \
sortPrimersByStartPosition.h \
sortUnacceptablePrimers.cpp \
sortUnacceptablePrimers.h \
subcloneTTemplate.cpp \
subcloneTTemplate.h \
sysdepend.h \
szGetTime.c \
szGetTime.h \
szWhichStrand.h \
tag.cpp \
tag.h \
tagSNPs.cpp \
tagSNPs.h \
tagTypes.cpp \
tagTypes.h \
tagsGotoList.cpp \
tagsGotoList.h \
teditor.cpp \
teditor.h \
teditor_types.h \
tedwin.cpp \
tedwin.h \
templateForMinilibrary.h \
templatesSortedByLibrary.h \
templatesSortedByName.h \
terminateIfDirectoryIsNotWritable.cpp \
terminateIfDirectoryIsNotWritable.h \
terminateIfNoPhdDir.cpp \
terminateIfNoPhdDir.h \
testReadPhdBall.cpp \
testReadPhdBall.h \
textbox.cpp \
textbox.h \
textfield.cpp \
textfield.h \
tracefile.cpp \
tracefile.h \
transitionsTransversions.cpp \
transitionsTransversions.h \
translateRWCString.cpp \
translateRWCString.h \
trimWhitespace.h \
typeDef.h \
uGetCRC_9_digits.cpp \
uGetCRC_9_digits.h \
ucGetMaskForSpecies.h \
ucGetReadType.cpp \
ucGetReadType.h \
ucNormalQualityFrom9899Quality.h \
unalignedHighQualityRegionsGotoList.cpp \
unalignedHighQualityRegionsGotoList.h \
universalPrimerAutoFinishExpTagsSortedByTemplateName.cpp \
universalPrimerAutoFinishExpTagsSortedByTemplateName.h \
unpaddedFromPadded.cpp \
unpaddedFromPadded.h \
userDefinedTagFieldType.cpp \
userDefinedTagFieldType.h \
userDefinedTagField.cpp \
userDefinedTagField.h \
visibleLineForRestrictionFragments.cpp \
visibleLineForRestrictionFragments.h \
waitUntilDialogIsVisible.cpp \
waitUntilDialogIsVisible.h \
whatToDoWithSelectionTypes.h \
whichPrimersAreAcceptable.cpp \
whichPrimersAreAcceptable.h \
whichPrimersHaveAcceptableMeltingTemp.cpp \
whichPrimersHaveAcceptableMeltingTemp.h \
whichPrimersHaveAcceptableSelfMatch.cpp \
whichPrimersHaveAcceptableSelfMatch.h \
wholeAssemblyItem.cpp \
wholeAssemblyItem.h \
wholeReadItem.cpp \
wholeReadItem.h \
whyIsPrimerNotAcceptableTypes.h \
writeNewAceFileNameToFile.cpp \
writeNewAceFileNameToFile.h \
xsynchronize.cpp \
xsynchronize.h 

chmod a+x makeMainCPP.perl
chmod a+x parseConsedResources.perl
chmod a+x processReadme.perl
chmod a+x makeDependMelakwa.perl
chmod a+x makeNewG++.perl