/***************************************************************************** # 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. # #*****************************************************************************/ // main.cpp_part3 //main.cpp_part3 starts static RWCString soUsage = "\ -ace\n\ -ace must be followed by a space and then the ace filename\n\ -socket\n\ -socket must be followed by a space and then a number (the local port number)\n\ -nophd\n\ -autoFinish\n\ -doExperiments\n\ -autoPCRAmplify\n\ -autoPCRAmplify must be followed by a space and then the name of the file of primer regions\n\ -justCheckAutoFinishReads\n\ -id\n\ -id must be followed by a space and then the id\n\ -contig\n\ -contig must be followed by a space and then the contig name\n\ -fileNamesFile\n\ -filenamesFile must be followed by a space and then the name of the file to contain the filenames\n\ -read_only\n\ -addNewReads\n\ -addNewReads must be followed by a space and then the name of the file containing the reads to be added\n\ -addReads\n\ -addReads must be followed by a space and then the name of the file containing a list of the cross_match alignment files\n\ -chem\n\ -chem must be followed by a space and then the chemistry which can be one of solexa, 454, or Sanger\n\ -autoEdit\n\ -newAceFileName\n\ -newAceFilename must be followed by a space and then the name of the ace file to be created\n\ -autoReport\n\ -nav\n\ -nav must be followed by a space and then the name of the custom navigation file\n\ -allowTimestampMismatch\n\ -mainContigPos\n\ -maincontigpos must be followed by a space and then the unpadded consensus position of the main contig\n\ -solexa2PhdBall\n\ -solexa2PhdBall must be followed by a space and then the name of a file containing the name of the solexa fastq files.\n\ -phdBallFOF\n\ -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.\n\ -selectRegions\n\ -selectRegions must be followed by a space and then the name of the regions file\n\ -alignments\n\ -alignments must be followed by a space and then the name of an fof of alignments files for -selectRegions\n\ -phdBall2Fasta\n\ -phdBall2Fasta must be followed by a space and then the name of the phd ball\n\ -fasta\n\ -fasta must be followed by a space and then the name of the output fasta file\n\ -fastq\n\ -fastq must be followed by a space and then the name of the output fastq file\n\ -testReadPhdBall\n\ -testReadPhdBall must be followed by a space and then the phdball to be read for testing purposes\n\ -removeReads\n\ -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\n\ -removeContigs\n\ -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\n\ -printDefaultResources\n\ -sff2PhdBall\n\ -sff2PhdBall must be followed by a space and then full path of the sff file\n\ -phdBall\n\ -phdBall must be followed by a space and then the full path of the phd ball\n\ -fof\n\ -fof must be followed by a space and then the name of a file containing read names\n\ -editConsedrc\n\ -changeConsensus\n\ -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\n\ -snpGenome\n\ -snpGenome must be followed by a space and then the full path of the snp table in ucsc format\n\ -genome\n\ -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.\n\ -valid\n\ -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.\n\ -diffChromosomes\n\ -diffChromosomes must be followed by a space and then the full or relative path of the other directory containing the chromosome files\n\ -addFlowcells\n\ -addFlowcells must be followed by a space and then the full or relative path of file containing flowcell lines\n\ -controlFile\n\ -controlFile must be followed by a space and then the full or relative path of the control file\n\ -fixContigEnds\n\ -contigEndsFOF\n\ -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)\n\ -geneClassifications\n\ -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\n\ -chromosomesFOF\n\ -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\n\ -knownGene\n\ -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\n\ -phaster2PhdBall\n\ -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 )\n\ -phasterLocations\n\ -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)\n\ -phyloFOF\n\ -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\n\ -miscProgram\n\ ";