BEGIN_GROUPS nError error_using_aszWhatIsRunning nGraphicalConsedIsRunning graphical_consed nAutoFinishIsRunning -autoFinish nAutoEditIsRunning -autoEdit nAutoReportIsRunning -autoReport nAutoPCRAmplifyIsRunning -autoPCRAmplify nAddReadsIsRunning -addReads nAddNewReadsIsRunning -addNewReads nAddAlignedSequenceIsRunning -addAlignedSequence nPrintSingleSignalIsRunning -singleSignal nTagSNPsIsRunning -tagSNPs nSolexa2PhdBallIsRunning -solexa2PhdBall nSelectRegionsIsRunning -selectRegions nPhdBall2FastaIsRunning -phdBall2Fasta nRemoveReadsIsRunning -removeReads nRemoveContigsIsRunning -removeContigs nPrintAllDefaultResources -printDefaultResources nSff2PhdBallIsRunning -sff2PhdBall nTestReadPhdBallIsRunning -testReadPhdBall nEditConsedrcIsRunning -editConsedrc nChangeConsensusIsRunning -changeConsensus nSnpGenomeIsRunning -snpGenome nDiffChromosomesIsRunning -diffChromosomes nAddFlowcellsIsRunning -addFlowcells nFixContigEndsIsRunning -fixContigEnds nGeneClassificationsIsRunning -geneClassifications nPhaster2PhdBallIsRunning -phaster2PhdBall nMiscProgramIsRunning -miscProgram END_GROUPS -ace bool bAceFileOnCommandLine ?group ?-ace show: yes FileName filAceFileToOpen -ace must be followed by a space and then the ace filename -socket bool bCreateSocketToControlConsed graphical_consed ?-ace show: yes RWCString soSocketToControlConsedLocalPortNumber -socket must be followed by a space and then a number (the local port number) -nophd bool bNoPhdFiles ?group ?-ace show: yes -autoFinish bool bAutomatedFinishProgram -autoFinish -ace show: yes -doExperiments bool bDoExperiments -autoFinish ?-ace show: yes -autoPCRAmplify bool bAutoPCRAmplify -autoPCRAmplify -ace show: yes FileName filFileOfPrimerRegions -autoPCRAmplify must be followed by a space and then the name of the file of primer regions -justCheckAutoFinishReads bool bJustCheckAutoFinishReads -autoFinish ?-ace show: yes -id bool bID -autoFinish ?-ace show: yes RWCString soID -id must be followed by a space and then the id -contig bool bContigSpecified -autoFinish ?-ace show: yes RWCString soContig -contig must be followed by a space and then the contig name -fileNamesFile bool bFileNamesFile -autoFinish ?-ace show: yes RWCString soFilenamesFile -filenamesFile must be followed by a space and then the name of the file to contain the filenames -fileOfPhdFiles bool bFileOfPhdFiles ?group ?-ace show: no (obsolete) FileName filFileOfPhdFiles -fileOfPhdFiles must be followed by a space and then the name of the file of phd files -terminate bool bTerminateAfterStartup ?group ?-ace show: no -read_only bool bReadOnly ?group ?-ace show: yes -addNewReads bool bAddNewReads -addNewReads -ace show: yes FileName filFileOfReadsOrPhdsToAdd -addNewReads must be followed by a space and then the name of the file containing the reads to be added -addReads bool bAddReads -addReads -ace show: yes FileName filAddNewReadsAlignmentsFOF -addReads must be followed by a space and then the name of the file containing a list of the cross_match alignment files -chem bool bChem -addReads ?-ace show: yes RWCString soChemistry -chem must be followed by a space and then the chemistry which can be one of solexa, 454, or Sanger -autoEdit bool bAutoEdit -autoEdit -ace show: yes -newAceFileName -newAceFile bool bNewAceFileName -autoEdit -addAlignedSequence -tagSNPs -addReads -addNewReads -removeReads -removeContigs -changeConsensus -ace show: yes FileName filNewAceFile -newAceFilename must be followed by a space and then the name of the ace file to be created -addAlignedSequence bool bAddAlignedSequence -addAlignedSequence -ace show: no FileName filAlignmentFastaFile -addAlignedSequence must be followed by a space and then the name of the fasta file created by alignment2Ace.perl -tagSNPs bool bTagSNPs -tagSNPs -ace show: no FileName filFileOfReadsOrPhdsToAddForTagSNPs -tagSNPs must be followed by a space and then the name of the fof of SNP reads -phdWithWRItem bool bPhdWithWRItem -addAlignedSequence ?-ace show: no FileName filPhdFileWithWRItem -phdWithWRItem must be followed by a space and then the name of the phd file containing the WR Item specifying the genomic region of the assembly -autoReport bool bAutoReport -autoReport -ace show: yes -nav bool bCustomNavigation graphical_consed -ace show: yes FileName filCustomNavigation -nav must be followed by a space and then the name of the custom navigation file -allowTimestampMismatch bool bAllowTimestampMismatch ?group ?-ace show: yes -singleSignal bool bPrintSingleSignal -singleSignal -ace show: no RWCString soUnpaddedConsPosForSingleSignal -singleSignal must be followed by a space and then the unpadded consensus position -mainContigPos bool bMainContigPos graphical_consed -ace show: yes RWCString soUnpaddedConsPos -maincontigpos must be followed by a space and then the unpadded consensus position of the main contig -solexa2PhdBall bool bSolexa2PhdBall -solexa2PhdBall no-ace show: yes FileName filSolexaFOF -solexa2PhdBall must be followed by a space and then the name of a file containing the name of the solexa fastq files. -phdBallFOF bool bNewPhdBallFOF -solexa2PhdBall -sff2PhdBall -phaster2PhdBall ?-ace show: yes FileName filNewPhdBallFOF -phdBallFOF must be followed by a space and then the name of the phdballfof to be created. This file contains a list of all of the phdballs created. -selectRegions bool bSelectRegions -selectRegions -ace show: yes FileName filRegionsFile -selectRegions must be followed by a space and then the name of the regions file -alignments bool bAlignments -selectRegions -ace show: yes FileName filSelectRegionsAlignmentsFOF -alignments must be followed by a space and then the name of an fof of alignments files for -selectRegions -phdBall2Fasta bool bPhdBall2Fasta -phdBall2Fasta no-ace show: yes FileName filPhdBall -phdBall2Fasta must be followed by a space and then the name of the phd ball -fasta bool bFasta -phdBall2Fasta no-ace show: yes FileName filFasta -fasta must be followed by a space and then the name of the output fasta file -fastq bool bFastq -phdBall2Fasta no-ace show: yes FileName filFastq -fastq must be followed by a space and then the name of the output fastq file -testReadPhdBall bool bTestReadPhdBall -testReadPhdBall no-ace show: yes FileName filPhdBallForTestRead -testReadPhdBall must be followed by a space and then the phdball to be read for testing purposes -removeReads bool bRemoveReads -removeReads -ace show: yes FileName filReadsToBeRemoved -removeReads must be followed by a space and then the file containing the reads to be removed. Use consed.removeReadsPutIntoOwnContig: true/false to determine whether the removed reads are just put into their own contigs or completely removed -removeContigs bool bRemoveContigs -removeContigs -ace show: yes FileName filContigsToBeRemoved -removeContigs must be followed by a space and then the file containing the contigs to be removed. Use consed.removeReadsPutIntoOwnContig: true/false to determine whether the removed reads are just put into their own contigs or completely removed -printDefaultResources bool bPrintDefaultResources -printDefaultResources no-ace show: yes -sff2PhdBall bool bSff2PhdBall -sff2PhdBall no-ace show: yes FileName filSffFile -sff2PhdBall must be followed by a space and then full path of the sff file -phdBall bool bPhdBall -sff2PhdBall ?-ace show: yes FileName filNewPhdBall -phdBall must be followed by a space and then the full path of the phd ball -fof bool bFOF -sff2PhdBall ?-ace show: yes FileName filFOF -fof must be followed by a space and then the name of a file containing read names -editConsedrc bool bEditConsedrc -editConsedrc no-ace show: yes -changeConsensus bool bChangeConsensus -changeConsensus -ace show: yes FileName filChangeConsensus -changeConsensus must be followed by a space and then the name of the file with lines like this: Contig21 28-30 x where Contig21 is the contig, 28-30 are the unpadded positions and x is the new base. To change a pad (let's say at padded position 35, specify this as *35 as in Contig21 *35-*40 c -snpGenome bool bSnpGenome -snpGenome no-ace show: yes FileName filSnps -snpGenome must be followed by a space and then the full path of the snp table in ucsc format -genome bool bGenome -snpGenome no-ace show: yes FileName filGenome -genome is used by -snpGenome. It must be followed by a space and then a file that has 3 columns for each chromosome: the name of the chromosome in the snp file, the full path of the corresponding chromosome in fasta format, and the full path of the snp-annotated chromosome to be created. -valid bool bValid -snpGenome no-ace show: yes FileName filValidation -valid is used by -snpGenome. It must be followed by a space and then a file that lists, one per line, each validation combination for which *no* snps are to be used. -diffChromosomes bool bDiffChromosomes -diffChromosomes no-ace show: yes FileName filOtherDirectory -diffChromosomes must be followed by a space and then the full or relative path of the other directory containing the chromosome files -addFlowcells bool bAddFlowcells -addFlowcells no-ace show: yes FileName filFlowcellsToAdd -addFlowcells must be followed by a space and then the full or relative path of file containing flowcell lines -controlFile bool bControlFile -addFlowcells no-ace show: yes FileName filControlFile -controlFile must be followed by a space and then the full or relative path of the control file -fixContigEnds bool bFixContigEnds -fixContigEnds -ace show: yes -contigEndsFOF bool bContigEndsFOF -fixContigEnds -ace show: yes FileName filContigEndsFOF -contigEndsFOF must be followed by a space and then the full or relative path of a file which each line having (contig name) (left or right) -geneClassifications bool bGeneClassifications -geneClassifications no-ace show: yes FileName filGenomicLocations -geneClassifications must be followed by a space and then the full or relative path of the list of genomic locations in the format chr1 345671 -chromosomesFOF bool bChromosomesFOF -geneClassifications no-ace show: yes FileName filChromosomesFOF -chromosomesFOF must be followed by a space and then the full or relative path of a file containing the full or relative paths of the chromosomes in fasta format -knownGene bool bKnownGene -geneClassifications no-ace show: yes FileName filKnownGene -knownGene must be followed by a space and then the full or relative path of a file containing the full or relative paths of the knownGene.txt file -phaster2PhdBall bool bPhaster2PhdBall -phaster2PhdBall no-ace show: yes FileName filPhasterFOF -phaster2PhdBall must be followed by a space and then the full or relative path of a file containing a list of phaster output files (assumes cref2 and -report_type:2 ) -phasterLocations bool bPhasterLocations -phaster2PhdBall no-ace show: yes FileName filPhasterLocations -phasterLocations must be followed by a space and then the full or relative path of a file containing a list of locations in the form (full phaster genomic location) (chromosome) (1-based chromosome position) -phyloFOF bool bPhyloFOF -geneClassifications no-ace show: yes FileName filPhyloFOF -phyloFOF must be followed by a space and then the full or relative path of a file containing the full or relative path of phyloP conservation score files in wig format such as chr11.phyloP44way.wigFix.gz -miscProgram bool bMiscProgram -miscProgram no-ace show: yes