/*****************************************************************************
# 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
//
// main routine for consEd application
//
//
// main.cpp_part1
// edit the following for new applications: main.cpp_part1, main.cpp_part11
// you can also edit main.cpp_part8 for compatibility between arguments
#include <new.h>
#include <setjmp.h>
#include <signal.h>
#include <stdlib.h>
#include <sys/utsname.h>
#include <time.h>
#include <unistd.h>
#include "addAlignedSequence.h"
#include "addNewReads.h"
#include "addNewReadsAutomated.h"
#include "addNewReadsWithExistingAlignments.h"
#include "assemblyView.h"
#include "autoEdit.h"
#include "autoFinish.h"
#include "autoPCRAmplify.h"
#include "autoReport.h"
#include "bIsNumericMaybeWithWhitespace.h"
#include "checkLicenseKey.h"
#include "checkVariableLengthLimit.h"
#include "consed.h"
#include "consedParameters.h"
#include "consedResources.h"
#include "consedResources.h"
#include "consed_version.h"
#include "contigwin.h"
#include "fileDefines.h"
#include "guiTopWindow.h"
#include "guiapp.h"
#include "listOfLibraries.h"
#include "maybeTerminateIfAnotherReadWriteConsed.h"
#include "mbt_exception.h"
#include "perhapsCreateSocketToControlConsed.h"
#include "printMemory.h"
#include "printSingleSignal.h"
#include "printTime.h"
#include "readAndProcessReadPrefixFile.h"
#include "rwctokenizer.h"
#include "saveTagTypes.h"
#include "setComplementBaseTable.h"
#include "setErrorRateFromQuality.h"
#include "setNotACGTTable.h"
#include "setNumberFromBaseTable.h"
#include "solexa2PhdBall.h"
#include "sysdepend.h"
#include "tagSNPs.h"
#include "terminateIfNoPhdDir.h"
#include "whatIsRunning.h"
#include "phdBall2Fasta.h"
#include "testReadPhdBall.h"
#include "removeReads.h"
#include "removeContigs.h"
#include "printDefaultResources.h"
#include "sff2PhdBall.h"
#include "guiEditResourcesStandalone.h"
#include "defaultResourcesDefinition.h"
#include "batchChangeConsensus.h"
#include "snpGenome.h"
#include "diffChromosomes.h"
#include "nextPhredPipeline.h"
#include "fixContigEnds.h"
#include "geneClassifications.h"
#include "phaster2PhdBall.h"
#include "miscProgram.h"
// definition for soEmptyString.h
RWCString soEmptyString = "";
bool bNoBaseSeg = false;
bool bNoSetSequence = false;
bool bNoFragments = false;
bool bNoListOfFragments = false;
bool bUnsortedBaseSegArray = false;
bool bUsingPhdFiles = true;
bool bReadOnly = false;
int nNumberOfErrorWindowsCurrentlyUp = 0; // global, used by
// popupInfoOrErrorMessageNoFormat.cpp
jmp_buf jmpBuffer;
const int nErrorReturn = 1;
static void handleSegmentationFault( int nSigNo ) {
fprintf( stderr, "Error from consed: segmentation fault. Attempting to continue\n" );
longjmp( jmpBuffer, nErrorReturn );
}
static bool bEstablishErrorHandler() {
if ( setjmp( jmpBuffer ) == nErrorReturn ) {
// just returned from an error
if ( setjmp( jmpBuffer ) != 0 ) {
cerr << "can't establish setjmp for handler of segmentation faults" << endl;
}
}
else if ( setjmp( jmpBuffer ) == 0 ) {
if ( signal( SIGSEGV, handleSegmentationFault ) == SIG_ERR ) {
cerr << "can't establish handler for segmentation faults" << endl;
}
return( true );
}
else {
cerr << "can't establish setjmp for handler of segmentation faults2" << endl;
}
return( false );
}
static void myNewHandler() {
printMemory( "In new memory handler" );
cerr<< "Consed: out of memory on heap (datasize)" << endl;
cerr<< "new threw an exception--you have run out of memory" << endl;
cerr<< "There is not enough datasize (heap)." << endl;
cerr<< "There may not be enough physical memory, or else" << endl;
cerr<< "there may be a software limit imposed on this process." << endl;
cerr<< "With tcsh, use type: limit to see what you are currently using." << endl;
cerr<< "Then type: limit datasize unlimited " << endl << ends;
cerr.flush();
ostrstream ost;
ost << "Consed: out of memory on heap (datasize)" << endl;
ost << "new threw an exception--you have run out of memory" << endl;
ost << "There is not enough datasize (heap)." << endl;
ost << "There may not be enough physical memory, or else" << endl;
ost << "there may be a software limit imposed on this process." << endl;
ost << "With tcsh, use type: limit to see what you are currently using." << endl;
ost << "Then type: limit datasize unlimited " << endl << ends;
SysRequestFailed sys( ost.str() );
throw( sys );
}
static void checkIfOperatingSystemIsOK() {
struct utsname myUtsname;
int nError = uname( &myUtsname );
if ( nError != -1 ) {
RWCString soOperatingSystem;
soOperatingSystem.getField( myUtsname.sysname, 9 );
soOperatingSystem.toLower();
if ( soOperatingSystem == "linux" ) {
RWCString soRelease;
soRelease.getField( myUtsname.release, 9 );
RWCString soVersion;
soVersion.getField( myUtsname.version, 9 );
// cerr << "release: " << soRelease << " version: " << soVersion << endl;
// check that this is 2.4 or better
// current version is 2.4.2-2sm
// Algorithm: look for the first character that isn't
// a [0-9] or "." and just consider that portion. Separate it
// by "." If the first number is greater than 3, accept. Otherwise
// it must be a 2 and look at the next number. If the next
// number is more than a 4, accept, otherwise it must be a 4 and
// look at the next number. The next number must be a 2 or greater
// in this case.
size_t nFirstBad = strspn( soRelease.data(), "0123456789." );
soRelease.truncate( nFirstBad );
RWCTokenizer tok( soRelease );
RWCString soFirst = tok('.');
RWCString soSecond = tok('.');
RWCString soThird = tok('.' );
int nFirst;
assert( bIsNumericMaybeWithWhitespace( soFirst, nFirst ) );
if ( nFirst > 2 )
return; // we are fine.
if ( nFirst < 2 ) {
cerr << "Sorry: the linux kernel must be version 2.4.2 or better. Type \"uname -a\" to find your current version. (1)" << endl;
exit( -1 );
}
// if reached here, must be version 2.?.?
int nSecond;
assert( bIsNumericMaybeWithWhitespace( soSecond, nSecond ) );
if ( nSecond > 4 )
return; // we are fine
if ( nSecond < 4 ) {
cerr << "Sorry: the linux kernel must be version 2.4.2 or better. Type \"uname -a\" to find your current version. (2)" << endl;
exit( -1 );
}
int nThird;
assert( bIsNumericMaybeWithWhitespace( soThird, nThird ) );
if ( nThird >= 2 )
return; // we are fine
// if reached here, the user is using an operating system that is
// too old.
cerr << "Sorry: the linux kernel must be version 2.4.2 or better. Type \"uname -a\" to find your current version. (3)" << endl;
exit( -1 );
}
else if ( soOperatingSystem == "darwin" ) {
RWCString soRelease;
soRelease.getField( myUtsname.release, 9 );
cerr << "Darwin Version: " << soRelease << endl;
size_t nFirstBad = strspn( soRelease.data(), "0123456789." );
soRelease.truncate( nFirstBad );
RWCTokenizer tok( soRelease );
RWCString soFirst = tok('.');
RWCString soSecond = tok('.');
RWCString soThird = tok('.' );
int nVersion;
if (!bIsNumericMaybeWithWhitespace( soFirst, nVersion ) ) {
return; // don't know if we are ok, but don't know we are not ok
}
if ( nVersion < 6 ) {
cerr << "Sorry: if you are running Macosx, you must be running version 10.2 or better (Darwin kernel 6.0 or better)" << endl;
exit( -1 );
}
}
}
}
// 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\
";
// main.cpp_part4
int main(int nArgc, char* argv[]) {
bool bAceFileOnCommandLine = false;
FileName filAceFileToOpen;
bool bCreateSocketToControlConsed = false;
RWCString soSocketToControlConsedLocalPortNumber;
bool bNoPhdFiles = false;
bool bAutomatedFinishProgram = false;
bool bDoExperiments = false;
bool bAutoPCRAmplify = false;
FileName filFileOfPrimerRegions;
bool bJustCheckAutoFinishReads = false;
bool bID = false;
RWCString soID;
bool bContigSpecified = false;
RWCString soContig;
bool bFileNamesFile = false;
RWCString soFilenamesFile;
bool bFileOfPhdFiles = false;
FileName filFileOfPhdFiles;
bool bTerminateAfterStartup = false;
bool bReadOnly = false;
bool bAddNewReads = false;
FileName filFileOfReadsOrPhdsToAdd;
bool bAddReads = false;
FileName filAddNewReadsAlignmentsFOF;
bool bChem = false;
RWCString soChemistry;
bool bAutoEdit = false;
bool bNewAceFileName = false;
FileName filNewAceFile;
bool bAddAlignedSequence = false;
FileName filAlignmentFastaFile;
bool bTagSNPs = false;
FileName filFileOfReadsOrPhdsToAddForTagSNPs;
bool bPhdWithWRItem = false;
FileName filPhdFileWithWRItem;
bool bAutoReport = false;
bool bCustomNavigation = false;
FileName filCustomNavigation;
bool bAllowTimestampMismatch = false;
bool bPrintSingleSignal = false;
RWCString soUnpaddedConsPosForSingleSignal;
bool bMainContigPos = false;
RWCString soUnpaddedConsPos;
bool bSolexa2PhdBall = false;
FileName filSolexaFOF;
bool bNewPhdBallFOF = false;
FileName filNewPhdBallFOF;
bool bSelectRegions = false;
FileName filRegionsFile;
bool bAlignments = false;
FileName filSelectRegionsAlignmentsFOF;
bool bPhdBall2Fasta = false;
FileName filPhdBall;
bool bFasta = false;
FileName filFasta;
bool bFastq = false;
FileName filFastq;
bool bTestReadPhdBall = false;
FileName filPhdBallForTestRead;
bool bRemoveReads = false;
FileName filReadsToBeRemoved;
bool bRemoveContigs = false;
FileName filContigsToBeRemoved;
bool bPrintDefaultResources = false;
bool bSff2PhdBall = false;
FileName filSffFile;
bool bPhdBall = false;
FileName filNewPhdBall;
bool bFOF = false;
FileName filFOF;
bool bEditConsedrc = false;
bool bChangeConsensus = false;
FileName filChangeConsensus;
bool bSnpGenome = false;
FileName filSnps;
bool bGenome = false;
FileName filGenome;
bool bValid = false;
FileName filValidation;
bool bDiffChromosomes = false;
FileName filOtherDirectory;
bool bAddFlowcells = false;
FileName filFlowcellsToAdd;
bool bControlFile = false;
FileName filControlFile;
bool bFixContigEnds = false;
bool bContigEndsFOF = false;
FileName filContigEndsFOF;
bool bGeneClassifications = false;
FileName filGenomicLocations;
bool bChromosomesFOF = false;
FileName filChromosomesFOF;
bool bKnownGene = false;
FileName filKnownGene;
bool bPhaster2PhdBall = false;
FileName filPhasterFOF;
bool bPhasterLocations = false;
FileName filPhasterLocations;
bool bPhyloFOF = false;
FileName filPhyloFOF;
bool bMiscProgram = false;
// main.cpp_part5
checkIfOperatingSystemIsOK();
RWCString soCommandLine;
int n;
for( n = 0; n < nArgc; ++n ) {
soCommandLine += argv[n];
soCommandLine += " ";
}
checkLicenseKey();
set_new_handler( myNewHandler );
checkVariableLengthLimit();
setComplementBaseTable();
setNumberFromBaseTable();
setNotACGTTable();
// main.cpp_part6 start
int nWhatIsRunning = nGraphicalConsedIsRunning;
// nWhatIsRunning might be changed below--
// nGraphicalConsedIsRunning is just the default
for( n = 1; n < nArgc; ++n ) {
RWCString soLowerCaseArg( argv[n] );
soLowerCaseArg.toLower();
if ( soLowerCaseArg % aszWhatIsRunning[ 2 ] ) {
// check if a group has already been assigned
if ( nWhatIsRunning != nGraphicalConsedIsRunning ) {
cerr << "Fatal Error: arguments " << aszWhatIsRunning[ nWhatIsRunning ] << " and " << argv[n] << " are mutually incompatible" << endl;
exit( -1 );
}
nWhatIsRunning = 2;
}
if ( soLowerCaseArg % aszWhatIsRunning[ 3 ] ) {
// check if a group has already been assigned
if ( nWhatIsRunning != nGraphicalConsedIsRunning ) {
cerr << "Fatal Error: arguments " << aszWhatIsRunning[ nWhatIsRunning ] << " and " << argv[n] << " are mutually incompatible" << endl;
exit( -1 );
}
nWhatIsRunning = 3;
}
if ( soLowerCaseArg % aszWhatIsRunning[ 4 ] ) {
// check if a group has already been assigned
if ( nWhatIsRunning != nGraphicalConsedIsRunning ) {
cerr << "Fatal Error: arguments " << aszWhatIsRunning[ nWhatIsRunning ] << " and " << argv[n] << " are mutually incompatible" << endl;
exit( -1 );
}
nWhatIsRunning = 4;
}
if ( soLowerCaseArg % aszWhatIsRunning[ 5 ] ) {
// check if a group has already been assigned
if ( nWhatIsRunning != nGraphicalConsedIsRunning ) {
cerr << "Fatal Error: arguments " << aszWhatIsRunning[ nWhatIsRunning ] << " and " << argv[n] << " are mutually incompatible" << endl;
exit( -1 );
}
nWhatIsRunning = 5;
}
if ( soLowerCaseArg % aszWhatIsRunning[ 6 ] ) {
// check if a group has already been assigned
if ( nWhatIsRunning != nGraphicalConsedIsRunning ) {
cerr << "Fatal Error: arguments " << aszWhatIsRunning[ nWhatIsRunning ] << " and " << argv[n] << " are mutually incompatible" << endl;
exit( -1 );
}
nWhatIsRunning = 6;
}
if ( soLowerCaseArg % aszWhatIsRunning[ 7 ] ) {
// check if a group has already been assigned
if ( nWhatIsRunning != nGraphicalConsedIsRunning ) {
cerr << "Fatal Error: arguments " << aszWhatIsRunning[ nWhatIsRunning ] << " and " << argv[n] << " are mutually incompatible" << endl;
exit( -1 );
}
nWhatIsRunning = 7;
}
if ( soLowerCaseArg % aszWhatIsRunning[ 8 ] ) {
// check if a group has already been assigned
if ( nWhatIsRunning != nGraphicalConsedIsRunning ) {
cerr << "Fatal Error: arguments " << aszWhatIsRunning[ nWhatIsRunning ] << " and " << argv[n] << " are mutually incompatible" << endl;
exit( -1 );
}
nWhatIsRunning = 8;
}
if ( soLowerCaseArg % aszWhatIsRunning[ 9 ] ) {
// check if a group has already been assigned
if ( nWhatIsRunning != nGraphicalConsedIsRunning ) {
cerr << "Fatal Error: arguments " << aszWhatIsRunning[ nWhatIsRunning ] << " and " << argv[n] << " are mutually incompatible" << endl;
exit( -1 );
}
nWhatIsRunning = 9;
}
if ( soLowerCaseArg % aszWhatIsRunning[ 10 ] ) {
// check if a group has already been assigned
if ( nWhatIsRunning != nGraphicalConsedIsRunning ) {
cerr << "Fatal Error: arguments " << aszWhatIsRunning[ nWhatIsRunning ] << " and " << argv[n] << " are mutually incompatible" << endl;
exit( -1 );
}
nWhatIsRunning = 10;
}
if ( soLowerCaseArg % aszWhatIsRunning[ 11 ] ) {
// check if a group has already been assigned
if ( nWhatIsRunning != nGraphicalConsedIsRunning ) {
cerr << "Fatal Error: arguments " << aszWhatIsRunning[ nWhatIsRunning ] << " and " << argv[n] << " are mutually incompatible" << endl;
exit( -1 );
}
nWhatIsRunning = 11;
}
if ( soLowerCaseArg % aszWhatIsRunning[ 12 ] ) {
// check if a group has already been assigned
if ( nWhatIsRunning != nGraphicalConsedIsRunning ) {
cerr << "Fatal Error: arguments " << aszWhatIsRunning[ nWhatIsRunning ] << " and " << argv[n] << " are mutually incompatible" << endl;
exit( -1 );
}
nWhatIsRunning = 12;
}
if ( soLowerCaseArg % aszWhatIsRunning[ 13 ] ) {
// check if a group has already been assigned
if ( nWhatIsRunning != nGraphicalConsedIsRunning ) {
cerr << "Fatal Error: arguments " << aszWhatIsRunning[ nWhatIsRunning ] << " and " << argv[n] << " are mutually incompatible" << endl;
exit( -1 );
}
nWhatIsRunning = 13;
}
if ( soLowerCaseArg % aszWhatIsRunning[ 14 ] ) {
// check if a group has already been assigned
if ( nWhatIsRunning != nGraphicalConsedIsRunning ) {
cerr << "Fatal Error: arguments " << aszWhatIsRunning[ nWhatIsRunning ] << " and " << argv[n] << " are mutually incompatible" << endl;
exit( -1 );
}
nWhatIsRunning = 14;
}
if ( soLowerCaseArg % aszWhatIsRunning[ 15 ] ) {
// check if a group has already been assigned
if ( nWhatIsRunning != nGraphicalConsedIsRunning ) {
cerr << "Fatal Error: arguments " << aszWhatIsRunning[ nWhatIsRunning ] << " and " << argv[n] << " are mutually incompatible" << endl;
exit( -1 );
}
nWhatIsRunning = 15;
}
if ( soLowerCaseArg % aszWhatIsRunning[ 16 ] ) {
// check if a group has already been assigned
if ( nWhatIsRunning != nGraphicalConsedIsRunning ) {
cerr << "Fatal Error: arguments " << aszWhatIsRunning[ nWhatIsRunning ] << " and " << argv[n] << " are mutually incompatible" << endl;
exit( -1 );
}
nWhatIsRunning = 16;
}
if ( soLowerCaseArg % aszWhatIsRunning[ 17 ] ) {
// check if a group has already been assigned
if ( nWhatIsRunning != nGraphicalConsedIsRunning ) {
cerr << "Fatal Error: arguments " << aszWhatIsRunning[ nWhatIsRunning ] << " and " << argv[n] << " are mutually incompatible" << endl;
exit( -1 );
}
nWhatIsRunning = 17;
}
if ( soLowerCaseArg % aszWhatIsRunning[ 18 ] ) {
// check if a group has already been assigned
if ( nWhatIsRunning != nGraphicalConsedIsRunning ) {
cerr << "Fatal Error: arguments " << aszWhatIsRunning[ nWhatIsRunning ] << " and " << argv[n] << " are mutually incompatible" << endl;
exit( -1 );
}
nWhatIsRunning = 18;
}
if ( soLowerCaseArg % aszWhatIsRunning[ 19 ] ) {
// check if a group has already been assigned
if ( nWhatIsRunning != nGraphicalConsedIsRunning ) {
cerr << "Fatal Error: arguments " << aszWhatIsRunning[ nWhatIsRunning ] << " and " << argv[n] << " are mutually incompatible" << endl;
exit( -1 );
}
nWhatIsRunning = 19;
}
if ( soLowerCaseArg % aszWhatIsRunning[ 20 ] ) {
// check if a group has already been assigned
if ( nWhatIsRunning != nGraphicalConsedIsRunning ) {
cerr << "Fatal Error: arguments " << aszWhatIsRunning[ nWhatIsRunning ] << " and " << argv[n] << " are mutually incompatible" << endl;
exit( -1 );
}
nWhatIsRunning = 20;
}
if ( soLowerCaseArg % aszWhatIsRunning[ 21 ] ) {
// check if a group has already been assigned
if ( nWhatIsRunning != nGraphicalConsedIsRunning ) {
cerr << "Fatal Error: arguments " << aszWhatIsRunning[ nWhatIsRunning ] << " and " << argv[n] << " are mutually incompatible" << endl;
exit( -1 );
}
nWhatIsRunning = 21;
}
if ( soLowerCaseArg % aszWhatIsRunning[ 22 ] ) {
// check if a group has already been assigned
if ( nWhatIsRunning != nGraphicalConsedIsRunning ) {
cerr << "Fatal Error: arguments " << aszWhatIsRunning[ nWhatIsRunning ] << " and " << argv[n] << " are mutually incompatible" << endl;
exit( -1 );
}
nWhatIsRunning = 22;
}
if ( soLowerCaseArg % aszWhatIsRunning[ 23 ] ) {
// check if a group has already been assigned
if ( nWhatIsRunning != nGraphicalConsedIsRunning ) {
cerr << "Fatal Error: arguments " << aszWhatIsRunning[ nWhatIsRunning ] << " and " << argv[n] << " are mutually incompatible" << endl;
exit( -1 );
}
nWhatIsRunning = 23;
}
if ( soLowerCaseArg % aszWhatIsRunning[ 24 ] ) {
// check if a group has already been assigned
if ( nWhatIsRunning != nGraphicalConsedIsRunning ) {
cerr << "Fatal Error: arguments " << aszWhatIsRunning[ nWhatIsRunning ] << " and " << argv[n] << " are mutually incompatible" << endl;
exit( -1 );
}
nWhatIsRunning = 24;
}
if ( soLowerCaseArg % aszWhatIsRunning[ 25 ] ) {
// check if a group has already been assigned
if ( nWhatIsRunning != nGraphicalConsedIsRunning ) {
cerr << "Fatal Error: arguments " << aszWhatIsRunning[ nWhatIsRunning ] << " and " << argv[n] << " are mutually incompatible" << endl;
exit( -1 );
}
nWhatIsRunning = 25;
}
if ( soLowerCaseArg % aszWhatIsRunning[ 26 ] ) {
// check if a group has already been assigned
if ( nWhatIsRunning != nGraphicalConsedIsRunning ) {
cerr << "Fatal Error: arguments " << aszWhatIsRunning[ nWhatIsRunning ] << " and " << argv[n] << " are mutually incompatible" << endl;
exit( -1 );
}
nWhatIsRunning = 26;
}
if ( soLowerCaseArg % aszWhatIsRunning[ 27 ] ) {
// check if a group has already been assigned
if ( nWhatIsRunning != nGraphicalConsedIsRunning ) {
cerr << "Fatal Error: arguments " << aszWhatIsRunning[ nWhatIsRunning ] << " and " << argv[n] << " are mutually incompatible" << endl;
exit( -1 );
}
nWhatIsRunning = 27;
}
}
// when reached here, we know that the user has not specified running more
// than one program and we have determined what that program is
if ( nWhatIsRunning != nGraphicalConsedIsRunning )
cerr << aszWhatIsRunning[ nWhatIsRunning ] << " will be run." << endl;
// main.cpp_part6b
for( n = 1; n < nArgc; ++n ) {
RWCString soLowerCaseArg( argv[n] );
soLowerCaseArg.toLower();
if ( strcmp(argv[n], "-noBaseSeg" )==0 ) {
cout << "bNoBaseSeg" << endl;
bNoBaseSeg = true;
}
else if ( strcmp(argv[n], "-help" ) == 0 ) {
cout << soUsage << endl;
cout << "for more help, bring up Consed and click on 'Help' or else see the README.txt file" << endl;
exit( 0 );
}
else if ( strcmp(argv[n], "-unsortedBaseSegArray" )==0 ) {
cout << "bUnsortedBaseSegArray" << endl;
bNoBaseSeg = true;
}
else if (strcmp( argv[n], "-noSetSequence" )==0 ) {
cout << "bNoSetSequence" << endl;
bNoSetSequence = true;
}
else if (strcmp( argv[n], "-noFragments" )==0 ) {
cout << "bNoFragments" << endl;
bNoFragments = true;
}
else if (strcmp( argv[n], "-noListOfFragments" )==0 ) {
cout << "bNoListOfFragments" << endl;
bNoListOfFragments = true;
}
else if ( soLowerCaseArg == "-v" ) {
cout << szConsedVersion << endl;
exit( 0 );
}
else if ( soLowerCaseArg == "-newphdball" ) {
cerr << "Fatal error: -newPhdBall is no longer supported. phdballs go into ../phdball_dir and are labelled phd.ball.1 phd.ball.2 ..." << endl;
exit( -1 );
}
// main.cpp_part7
else if ( soLowerCaseArg == "-ace" ) {
bAceFileOnCommandLine = true;
++n;
if ( n >= nArgc ) {
cerr << "Fatal Error: -ace must be followed by a space and then the ace filename" << endl;
exit( -1 );
}
filAceFileToOpen = argv[n];
}
else if ( soLowerCaseArg == "-socket" ) {
bCreateSocketToControlConsed = true;
++n;
if ( n >= nArgc ) {
cerr << "Fatal Error: -socket must be followed by a space and then a number (the local port number)" << endl;
exit( -1 );
}
soSocketToControlConsedLocalPortNumber = argv[n];
}
else if ( soLowerCaseArg == "-nophd" ) {
bNoPhdFiles = true;
}
else if ( soLowerCaseArg == "-autofinish" ) {
bAutomatedFinishProgram = true;
}
else if ( soLowerCaseArg == "-doexperiments" ) {
bDoExperiments = true;
}
else if ( soLowerCaseArg == "-autopcramplify" ) {
bAutoPCRAmplify = true;
++n;
if ( n >= nArgc ) {
cerr << "Fatal Error: -autoPCRAmplify must be followed by a space and then the name of the file of primer regions" << endl;
exit( -1 );
}
filFileOfPrimerRegions = argv[n];
}
else if ( soLowerCaseArg == "-justcheckautofinishreads" ) {
bJustCheckAutoFinishReads = true;
}
else if ( soLowerCaseArg == "-id" ) {
bID = true;
++n;
if ( n >= nArgc ) {
cerr << "Fatal Error: -id must be followed by a space and then the id" << endl;
exit( -1 );
}
soID = argv[n];
}
else if ( soLowerCaseArg == "-contig" ) {
bContigSpecified = true;
++n;
if ( n >= nArgc ) {
cerr << "Fatal Error: -contig must be followed by a space and then the contig name" << endl;
exit( -1 );
}
soContig = argv[n];
}
else if ( soLowerCaseArg == "-filenamesfile" ) {
bFileNamesFile = true;
++n;
if ( n >= nArgc ) {
cerr << "Fatal Error: -filenamesFile must be followed by a space and then the name of the file to contain the filenames" << endl;
exit( -1 );
}
soFilenamesFile = argv[n];
}
else if ( soLowerCaseArg == "-fileofphdfiles" ) {
bFileOfPhdFiles = true;
++n;
if ( n >= nArgc ) {
cerr << "Fatal Error: -fileOfPhdFiles must be followed by a space and then the name of the file of phd files" << endl;
exit( -1 );
}
filFileOfPhdFiles = argv[n];
}
else if ( soLowerCaseArg == "-terminate" ) {
bTerminateAfterStartup = true;
}
else if ( soLowerCaseArg == "-read_only" ) {
bReadOnly = true;
}
else if ( soLowerCaseArg == "-addnewreads" ) {
bAddNewReads = true;
++n;
if ( n >= nArgc ) {
cerr << "Fatal Error: -addNewReads must be followed by a space and then the name of the file containing the reads to be added" << endl;
exit( -1 );
}
filFileOfReadsOrPhdsToAdd = argv[n];
}
else if ( soLowerCaseArg == "-addreads" ) {
bAddReads = true;
++n;
if ( n >= nArgc ) {
cerr << "Fatal Error: -addReads must be followed by a space and then the name of the file containing a list of the cross_match alignment files" << endl;
exit( -1 );
}
filAddNewReadsAlignmentsFOF = argv[n];
}
else if ( soLowerCaseArg == "-chem" ) {
bChem = true;
++n;
if ( n >= nArgc ) {
cerr << "Fatal Error: -chem must be followed by a space and then the chemistry which can be one of solexa, 454, or Sanger" << endl;
exit( -1 );
}
soChemistry = argv[n];
}
else if ( soLowerCaseArg == "-autoedit" ) {
bAutoEdit = true;
}
else if ( ( soLowerCaseArg == "-newacefilename" ) || ( soLowerCaseArg == "-newacefile" )
) {
bNewAceFileName = true;
++n;
if ( n >= nArgc ) {
cerr << "Fatal Error: -newAceFilename must be followed by a space and then the name of the ace file to be created" << endl;
exit( -1 );
}
filNewAceFile = argv[n];
}
else if ( soLowerCaseArg == "-addalignedsequence" ) {
bAddAlignedSequence = true;
++n;
if ( n >= nArgc ) {
cerr << "Fatal Error: -addAlignedSequence must be followed by a space and then the name of the fasta file created by alignment2Ace.perl" << endl;
exit( -1 );
}
filAlignmentFastaFile = argv[n];
}
else if ( soLowerCaseArg == "-tagsnps" ) {
bTagSNPs = true;
++n;
if ( n >= nArgc ) {
cerr << "Fatal Error: -tagSNPs must be followed by a space and then the name of the fof of SNP reads" << endl;
exit( -1 );
}
filFileOfReadsOrPhdsToAddForTagSNPs = argv[n];
}
else if ( soLowerCaseArg == "-phdwithwritem" ) {
bPhdWithWRItem = true;
++n;
if ( n >= nArgc ) {
cerr << "Fatal Error: -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" << endl;
exit( -1 );
}
filPhdFileWithWRItem = argv[n];
}
else if ( soLowerCaseArg == "-autoreport" ) {
bAutoReport = true;
}
else if ( soLowerCaseArg == "-nav" ) {
bCustomNavigation = true;
++n;
if ( n >= nArgc ) {
cerr << "Fatal Error: -nav must be followed by a space and then the name of the custom navigation file" << endl;
exit( -1 );
}
filCustomNavigation = argv[n];
}
else if ( soLowerCaseArg == "-allowtimestampmismatch" ) {
bAllowTimestampMismatch = true;
}
else if ( soLowerCaseArg == "-singlesignal" ) {
bPrintSingleSignal = true;
++n;
if ( n >= nArgc ) {
cerr << "Fatal Error: -singleSignal must be followed by a space and then the unpadded consensus position" << endl;
exit( -1 );
}
soUnpaddedConsPosForSingleSignal = argv[n];
}
else if ( soLowerCaseArg == "-maincontigpos" ) {
bMainContigPos = true;
++n;
if ( n >= nArgc ) {
cerr << "Fatal Error: -maincontigpos must be followed by a space and then the unpadded consensus position of the main contig" << endl;
exit( -1 );
}
soUnpaddedConsPos = argv[n];
}
else if ( soLowerCaseArg == "-solexa2phdball" ) {
bSolexa2PhdBall = true;
++n;
if ( n >= nArgc ) {
cerr << "Fatal Error: -solexa2PhdBall must be followed by a space and then the name of a file containing the name of the solexa fastq files." << endl;
exit( -1 );
}
filSolexaFOF = argv[n];
}
else if ( soLowerCaseArg == "-phdballfof" ) {
bNewPhdBallFOF = true;
++n;
if ( n >= nArgc ) {
cerr << "Fatal Error: -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." << endl;
exit( -1 );
}
filNewPhdBallFOF = argv[n];
}
else if ( soLowerCaseArg == "-selectregions" ) {
bSelectRegions = true;
++n;
if ( n >= nArgc ) {
cerr << "Fatal Error: -selectRegions must be followed by a space and then the name of the regions file" << endl;
exit( -1 );
}
filRegionsFile = argv[n];
}
else if ( soLowerCaseArg == "-alignments" ) {
bAlignments = true;
++n;
if ( n >= nArgc ) {
cerr << "Fatal Error: -alignments must be followed by a space and then the name of an fof of alignments files for -selectRegions" << endl;
exit( -1 );
}
filSelectRegionsAlignmentsFOF = argv[n];
}
else if ( soLowerCaseArg == "-phdball2fasta" ) {
bPhdBall2Fasta = true;
++n;
if ( n >= nArgc ) {
cerr << "Fatal Error: -phdBall2Fasta must be followed by a space and then the name of the phd ball" << endl;
exit( -1 );
}
filPhdBall = argv[n];
}
else if ( soLowerCaseArg == "-fasta" ) {
bFasta = true;
++n;
if ( n >= nArgc ) {
cerr << "Fatal Error: -fasta must be followed by a space and then the name of the output fasta file" << endl;
exit( -1 );
}
filFasta = argv[n];
}
else if ( soLowerCaseArg == "-fastq" ) {
bFastq = true;
++n;
if ( n >= nArgc ) {
cerr << "Fatal Error: -fastq must be followed by a space and then the name of the output fastq file" << endl;
exit( -1 );
}
filFastq = argv[n];
}
else if ( soLowerCaseArg == "-testreadphdball" ) {
bTestReadPhdBall = true;
++n;
if ( n >= nArgc ) {
cerr << "Fatal Error: -testReadPhdBall must be followed by a space and then the phdball to be read for testing purposes" << endl;
exit( -1 );
}
filPhdBallForTestRead = argv[n];
}
else if ( soLowerCaseArg == "-removereads" ) {
bRemoveReads = true;
++n;
if ( n >= nArgc ) {
cerr << "Fatal Error: -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" << endl;
exit( -1 );
}
filReadsToBeRemoved = argv[n];
}
else if ( soLowerCaseArg == "-removecontigs" ) {
bRemoveContigs = true;
++n;
if ( n >= nArgc ) {
cerr << "Fatal Error: -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" << endl;
exit( -1 );
}
filContigsToBeRemoved = argv[n];
}
else if ( soLowerCaseArg == "-printdefaultresources" ) {
bPrintDefaultResources = true;
}
else if ( soLowerCaseArg == "-sff2phdball" ) {
bSff2PhdBall = true;
++n;
if ( n >= nArgc ) {
cerr << "Fatal Error: -sff2PhdBall must be followed by a space and then full path of the sff file" << endl;
exit( -1 );
}
filSffFile = argv[n];
}
else if ( soLowerCaseArg == "-phdball" ) {
bPhdBall = true;
++n;
if ( n >= nArgc ) {
cerr << "Fatal Error: -phdBall must be followed by a space and then the full path of the phd ball" << endl;
exit( -1 );
}
filNewPhdBall = argv[n];
}
else if ( soLowerCaseArg == "-fof" ) {
bFOF = true;
++n;
if ( n >= nArgc ) {
cerr << "Fatal Error: -fof must be followed by a space and then the name of a file containing read names" << endl;
exit( -1 );
}
filFOF = argv[n];
}
else if ( soLowerCaseArg == "-editconsedrc" ) {
bEditConsedrc = true;
}
else if ( soLowerCaseArg == "-changeconsensus" ) {
bChangeConsensus = true;
++n;
if ( n >= nArgc ) {
cerr << "Fatal Error: -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" << endl;
exit( -1 );
}
filChangeConsensus = argv[n];
}
else if ( soLowerCaseArg == "-snpgenome" ) {
bSnpGenome = true;
++n;
if ( n >= nArgc ) {
cerr << "Fatal Error: -snpGenome must be followed by a space and then the full path of the snp table in ucsc format" << endl;
exit( -1 );
}
filSnps = argv[n];
}
else if ( soLowerCaseArg == "-genome" ) {
bGenome = true;
++n;
if ( n >= nArgc ) {
cerr << "Fatal Error: -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." << endl;
exit( -1 );
}
filGenome = argv[n];
}
else if ( soLowerCaseArg == "-valid" ) {
bValid = true;
++n;
if ( n >= nArgc ) {
cerr << "Fatal Error: -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." << endl;
exit( -1 );
}
filValidation = argv[n];
}
else if ( soLowerCaseArg == "-diffchromosomes" ) {
bDiffChromosomes = true;
++n;
if ( n >= nArgc ) {
cerr << "Fatal Error: -diffChromosomes must be followed by a space and then the full or relative path of the other directory containing the chromosome files" << endl;
exit( -1 );
}
filOtherDirectory = argv[n];
}
else if ( soLowerCaseArg == "-addflowcells" ) {
bAddFlowcells = true;
++n;
if ( n >= nArgc ) {
cerr << "Fatal Error: -addFlowcells must be followed by a space and then the full or relative path of file containing flowcell lines" << endl;
exit( -1 );
}
filFlowcellsToAdd = argv[n];
}
else if ( soLowerCaseArg == "-controlfile" ) {
bControlFile = true;
++n;
if ( n >= nArgc ) {
cerr << "Fatal Error: -controlFile must be followed by a space and then the full or relative path of the control file" << endl;
exit( -1 );
}
filControlFile = argv[n];
}
else if ( soLowerCaseArg == "-fixcontigends" ) {
bFixContigEnds = true;
}
else if ( soLowerCaseArg == "-contigendsfof" ) {
bContigEndsFOF = true;
++n;
if ( n >= nArgc ) {
cerr << "Fatal Error: -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)" << endl;
exit( -1 );
}
filContigEndsFOF = argv[n];
}
else if ( soLowerCaseArg == "-geneclassifications" ) {
bGeneClassifications = true;
++n;
if ( n >= nArgc ) {
cerr << "Fatal Error: -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" << endl;
exit( -1 );
}
filGenomicLocations = argv[n];
}
else if ( soLowerCaseArg == "-chromosomesfof" ) {
bChromosomesFOF = true;
++n;
if ( n >= nArgc ) {
cerr << "Fatal Error: -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" << endl;
exit( -1 );
}
filChromosomesFOF = argv[n];
}
else if ( soLowerCaseArg == "-knowngene" ) {
bKnownGene = true;
++n;
if ( n >= nArgc ) {
cerr << "Fatal Error: -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" << endl;
exit( -1 );
}
filKnownGene = argv[n];
}
else if ( soLowerCaseArg == "-phaster2phdball" ) {
bPhaster2PhdBall = true;
++n;
if ( n >= nArgc ) {
cerr << "Fatal Error: -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 )" << endl;
exit( -1 );
}
filPhasterFOF = argv[n];
}
else if ( soLowerCaseArg == "-phasterlocations" ) {
bPhasterLocations = true;
++n;
if ( n >= nArgc ) {
cerr << "Fatal Error: -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)" << endl;
exit( -1 );
}
filPhasterLocations = argv[n];
}
else if ( soLowerCaseArg == "-phylofof" ) {
bPhyloFOF = true;
++n;
if ( n >= nArgc ) {
cerr << "Fatal Error: -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" << endl;
exit( -1 );
}
filPhyloFOF = argv[n];
}
else if ( soLowerCaseArg == "-miscprogram" ) {
bMiscProgram = true;
}
// main.cpp_part8
else if ( soLowerCaseArg == "-dumpdefaultresources" ) {
bPrintDefaultResources = true;
}
else if ( soLowerCaseArg == "-printconsedresources" ) {
bPrintDefaultResources = true;
}
else if ( soLowerCaseArg == "-printconsedrcresources" ) {
bPrintDefaultResources = true;
}
else if ( soLowerCaseArg == "-printconsedparameters" ) {
bPrintDefaultResources = true;
}
else if ( soLowerCaseArg == "-printconsedrcparameters" ) {
bPrintDefaultResources = true;
}
else {
cerr << "Error: do not recognize argument " << argv[n] << " lowercase: " << soLowerCaseArg << endl;
cout << soUsage << endl;
_exit( -1 );
}
} // for( n = 0; n < nArgc; ++n ) {
if ( bAddReads && !bChem ) {
cerr << "Fatal Error: if you specify -addReads, you must also specify -chem to give the type of chemistry of reads being added. At this time, each chemistry of reads must be added one at a time." << endl;
_exit( -1 );
}
if ( bSolexa2PhdBall && !bNewPhdBallFOF ) {
cerr << "Fatal Error: if you specify -solexa2PhdBall, you must also specify -phdBallFOF (file for this program to write the phdball filenames)" << endl;
_exit( -1 );
}
if ( bSelectRegions && !bAlignments ) {
cerr << "Fatal Error: if you specify -selectRegions, you must also specify -alignments (alignments file)" << endl;
_exit( -1 );
}
if ( bPhdBall2Fasta && !bFasta && !bFastq ) {
cerr << "Fatal Error: if you specify -phdBall2Fasta, you must also specify -fasta (fasta file) or -fastq (fastq file)" << endl;
_exit( -1 );
}
if ( bSff2PhdBall && !bPhdBall ) {
cerr << "Fatal Error: if you specify -sff2PhdBall, must also specify -phdBall (phdball full path)" << endl;
_exit( -1 );
}
if ( bSnpGenome && !bGenome ) {
cerr << "Fatal Error: if you specify -snpGenome, you must also specify -genome" << endl;
_exit( -1 );
}
if ( bSnpGenome && !bValid ) {
cerr << "Fatal Error: if you specify -snpGenome, you must also specify -valid" << endl;
_exit( -1 );
}
if ( bGeneClassifications && ! bChromosomesFOF ) {
cerr << "Fatal Error: if you specify -geneClassifications, you must also specify -chromosomesFOF" << endl;
_exit( -1 );
}
if ( bGeneClassifications && !bKnownGene ) {
cerr << "Fatal Error: if you specify -geneClassifications, you must also specify -knownGene" << endl;
_exit( -1 );
}
if ( bPhaster2PhdBall && !bPhasterLocations ) {
cerr << "Fatal Error: if you specify -phaster2PhdBall, you must also specify -phasterLocations" << endl;
_exit( -1 );
}
if ( bPhaster2PhdBall && !bNewPhdBallFOF ) {
cerr << "Fatal Error: if you specify -phaster2PhdBall, you must also specify -phdBallFOF (file for this program to write the phdball filenames)" << endl;
_exit( -1 );
}
if ( bNoPhdFiles ) {
cout << "Not using phd files" << endl;
}
if ( bAddFlowcells && !bControlFile ) {
cerr << "Fatal Error: if you specify -addFlowCell, you must also specify -controlFile" << endl;
_exit( -1 );
}
// main.cpp_part9
if ( bCreateSocketToControlConsed ) {
if ( ( nWhatIsRunning != nGraphicalConsedIsRunning )
) {
cerr << "-socket cannot be used with " << aszWhatIsRunning[ nWhatIsRunning ] << endl;
cerr << "-socket must only be used with: " << endl;
cerr << " graphical_consed" << endl;
exit( -1 );
}
}
if ( bDoExperiments ) {
if ( ( nWhatIsRunning != nAutoFinishIsRunning )
) {
cerr << "-doExperiments cannot be used with " << aszWhatIsRunning[ nWhatIsRunning ] << endl;
cerr << "-doExperiments must only be used with: " << endl;
cerr << " -autoFinish" << endl;
exit( -1 );
}
}
if ( bJustCheckAutoFinishReads ) {
if ( ( nWhatIsRunning != nAutoFinishIsRunning )
) {
cerr << "-justCheckAutoFinishReads cannot be used with " << aszWhatIsRunning[ nWhatIsRunning ] << endl;
cerr << "-justCheckAutoFinishReads must only be used with: " << endl;
cerr << " -autoFinish" << endl;
exit( -1 );
}
}
if ( bID ) {
if ( ( nWhatIsRunning != nAutoFinishIsRunning )
) {
cerr << "-id cannot be used with " << aszWhatIsRunning[ nWhatIsRunning ] << endl;
cerr << "-id must only be used with: " << endl;
cerr << " -autoFinish" << endl;
exit( -1 );
}
}
if ( bContigSpecified ) {
if ( ( nWhatIsRunning != nAutoFinishIsRunning )
) {
cerr << "-contig cannot be used with " << aszWhatIsRunning[ nWhatIsRunning ] << endl;
cerr << "-contig must only be used with: " << endl;
cerr << " -autoFinish" << endl;
exit( -1 );
}
}
if ( bFileNamesFile ) {
if ( ( nWhatIsRunning != nAutoFinishIsRunning )
) {
cerr << "-fileNamesFile cannot be used with " << aszWhatIsRunning[ nWhatIsRunning ] << endl;
cerr << "-fileNamesFile must only be used with: " << endl;
cerr << " -autoFinish" << endl;
exit( -1 );
}
}
if ( bChem ) {
if ( ( nWhatIsRunning != nAddReadsIsRunning )
) {
cerr << "-chem cannot be used with " << aszWhatIsRunning[ nWhatIsRunning ] << endl;
cerr << "-chem must only be used with: " << endl;
cerr << " -addReads" << endl;
exit( -1 );
}
}
if ( bNewAceFileName ) {
if ( ( nWhatIsRunning != nAutoEditIsRunning )
&& ( nWhatIsRunning != nAddAlignedSequenceIsRunning )
&& ( nWhatIsRunning != nTagSNPsIsRunning )
&& ( nWhatIsRunning != nAddReadsIsRunning )
&& ( nWhatIsRunning != nAddNewReadsIsRunning )
&& ( nWhatIsRunning != nRemoveReadsIsRunning )
&& ( nWhatIsRunning != nRemoveContigsIsRunning )
&& ( nWhatIsRunning != nChangeConsensusIsRunning )
) {
cerr << "-newAceFileName cannot be used with " << aszWhatIsRunning[ nWhatIsRunning ] << endl;
cerr << "-newAceFileName must only be used with: " << endl;
cerr << " -autoEdit" << endl;
cerr << " -addAlignedSequence" << endl;
cerr << " -tagSNPs" << endl;
cerr << " -addReads" << endl;
cerr << " -addNewReads" << endl;
cerr << " -removeReads" << endl;
cerr << " -removeContigs" << endl;
cerr << " -changeConsensus" << endl;
exit( -1 );
}
}
if ( bPhdWithWRItem ) {
if ( ( nWhatIsRunning != nAddAlignedSequenceIsRunning )
) {
cerr << "-phdWithWRItem cannot be used with " << aszWhatIsRunning[ nWhatIsRunning ] << endl;
cerr << "-phdWithWRItem must only be used with: " << endl;
cerr << " -addAlignedSequence" << endl;
exit( -1 );
}
}
if ( bCustomNavigation ) {
if ( ( nWhatIsRunning != nGraphicalConsedIsRunning )
) {
cerr << "-nav cannot be used with " << aszWhatIsRunning[ nWhatIsRunning ] << endl;
cerr << "-nav must only be used with: " << endl;
cerr << " graphical_consed" << endl;
exit( -1 );
}
}
if ( bMainContigPos ) {
if ( ( nWhatIsRunning != nGraphicalConsedIsRunning )
) {
cerr << "-mainContigPos cannot be used with " << aszWhatIsRunning[ nWhatIsRunning ] << endl;
cerr << "-mainContigPos must only be used with: " << endl;
cerr << " graphical_consed" << endl;
exit( -1 );
}
}
if ( bNewPhdBallFOF ) {
if ( ( nWhatIsRunning != nSolexa2PhdBallIsRunning )
&& ( nWhatIsRunning != nSff2PhdBallIsRunning )
&& ( nWhatIsRunning != nPhaster2PhdBallIsRunning )
) {
cerr << "-phdBallFOF cannot be used with " << aszWhatIsRunning[ nWhatIsRunning ] << endl;
cerr << "-phdBallFOF must only be used with: " << endl;
cerr << " -solexa2PhdBall" << endl;
cerr << " -sff2PhdBall" << endl;
cerr << " -phaster2PhdBall" << endl;
exit( -1 );
}
}
if ( bAlignments ) {
if ( ( nWhatIsRunning != nSelectRegionsIsRunning )
) {
cerr << "-alignments cannot be used with " << aszWhatIsRunning[ nWhatIsRunning ] << endl;
cerr << "-alignments must only be used with: " << endl;
cerr << " -selectRegions" << endl;
exit( -1 );
}
}
if ( bFasta ) {
if ( ( nWhatIsRunning != nPhdBall2FastaIsRunning )
) {
cerr << "-fasta cannot be used with " << aszWhatIsRunning[ nWhatIsRunning ] << endl;
cerr << "-fasta must only be used with: " << endl;
cerr << " -phdBall2Fasta" << endl;
exit( -1 );
}
}
if ( bFastq ) {
if ( ( nWhatIsRunning != nPhdBall2FastaIsRunning )
) {
cerr << "-fastq cannot be used with " << aszWhatIsRunning[ nWhatIsRunning ] << endl;
cerr << "-fastq must only be used with: " << endl;
cerr << " -phdBall2Fasta" << endl;
exit( -1 );
}
}
if ( bPhdBall ) {
if ( ( nWhatIsRunning != nSff2PhdBallIsRunning )
) {
cerr << "-phdBall cannot be used with " << aszWhatIsRunning[ nWhatIsRunning ] << endl;
cerr << "-phdBall must only be used with: " << endl;
cerr << " -sff2PhdBall" << endl;
exit( -1 );
}
}
if ( bFOF ) {
if ( ( nWhatIsRunning != nSff2PhdBallIsRunning )
) {
cerr << "-fof cannot be used with " << aszWhatIsRunning[ nWhatIsRunning ] << endl;
cerr << "-fof must only be used with: " << endl;
cerr << " -sff2PhdBall" << endl;
exit( -1 );
}
}
if ( bGenome ) {
if ( ( nWhatIsRunning != nSnpGenomeIsRunning )
) {
cerr << "-genome cannot be used with " << aszWhatIsRunning[ nWhatIsRunning ] << endl;
cerr << "-genome must only be used with: " << endl;
cerr << " -snpGenome" << endl;
exit( -1 );
}
}
if ( bValid ) {
if ( ( nWhatIsRunning != nSnpGenomeIsRunning )
) {
cerr << "-valid cannot be used with " << aszWhatIsRunning[ nWhatIsRunning ] << endl;
cerr << "-valid must only be used with: " << endl;
cerr << " -snpGenome" << endl;
exit( -1 );
}
}
if ( bControlFile ) {
if ( ( nWhatIsRunning != nAddFlowcellsIsRunning )
) {
cerr << "-controlFile cannot be used with " << aszWhatIsRunning[ nWhatIsRunning ] << endl;
cerr << "-controlFile must only be used with: " << endl;
cerr << " -addFlowcells" << endl;
exit( -1 );
}
}
if ( bContigEndsFOF ) {
if ( ( nWhatIsRunning != nFixContigEndsIsRunning )
) {
cerr << "-contigEndsFOF cannot be used with " << aszWhatIsRunning[ nWhatIsRunning ] << endl;
cerr << "-contigEndsFOF must only be used with: " << endl;
cerr << " -fixContigEnds" << endl;
exit( -1 );
}
}
if ( bChromosomesFOF ) {
if ( ( nWhatIsRunning != nGeneClassificationsIsRunning )
) {
cerr << "-chromosomesFOF cannot be used with " << aszWhatIsRunning[ nWhatIsRunning ] << endl;
cerr << "-chromosomesFOF must only be used with: " << endl;
cerr << " -geneClassifications" << endl;
exit( -1 );
}
}
if ( bKnownGene ) {
if ( ( nWhatIsRunning != nGeneClassificationsIsRunning )
) {
cerr << "-knownGene cannot be used with " << aszWhatIsRunning[ nWhatIsRunning ] << endl;
cerr << "-knownGene must only be used with: " << endl;
cerr << " -geneClassifications" << endl;
exit( -1 );
}
}
if ( bPhasterLocations ) {
if ( ( nWhatIsRunning != nPhaster2PhdBallIsRunning )
) {
cerr << "-phasterLocations cannot be used with " << aszWhatIsRunning[ nWhatIsRunning ] << endl;
cerr << "-phasterLocations must only be used with: " << endl;
cerr << " -phaster2PhdBall" << endl;
exit( -1 );
}
}
if ( bPhyloFOF ) {
if ( ( nWhatIsRunning != nGeneClassificationsIsRunning )
) {
cerr << "-phyloFOF cannot be used with " << aszWhatIsRunning[ nWhatIsRunning ] << endl;
cerr << "-phyloFOF must only be used with: " << endl;
cerr << " -geneClassifications" << endl;
exit( -1 );
}
}
// main.cpp_part10
if ( bAutomatedFinishProgram && !bAceFileOnCommandLine ) {
cerr << "Error: If you specify -autoFinish, you must also specify -ace (ace file)" << endl;
exit( -1 );
}
if ( bAutoPCRAmplify && !bAceFileOnCommandLine ) {
cerr << "Error: If you specify -autoPCRAmplify, you must also specify -ace (ace file)" << endl;
exit( -1 );
}
if ( bAddNewReads && !bAceFileOnCommandLine ) {
cerr << "Error: If you specify -addNewReads, you must also specify -ace (ace file)" << endl;
exit( -1 );
}
if ( bAddReads && !bAceFileOnCommandLine ) {
cerr << "Error: If you specify -addReads, you must also specify -ace (ace file)" << endl;
exit( -1 );
}
if ( bAutoEdit && !bAceFileOnCommandLine ) {
cerr << "Error: If you specify -autoEdit, you must also specify -ace (ace file)" << endl;
exit( -1 );
}
if ( bNewAceFileName && !bAceFileOnCommandLine ) {
cerr << "Error: If you specify -newAceFileName, you must also specify -ace (ace file)" << endl;
exit( -1 );
}
if ( bAddAlignedSequence && !bAceFileOnCommandLine ) {
cerr << "Error: If you specify -addAlignedSequence, you must also specify -ace (ace file)" << endl;
exit( -1 );
}
if ( bTagSNPs && !bAceFileOnCommandLine ) {
cerr << "Error: If you specify -tagSNPs, you must also specify -ace (ace file)" << endl;
exit( -1 );
}
if ( bAutoReport && !bAceFileOnCommandLine ) {
cerr << "Error: If you specify -autoReport, you must also specify -ace (ace file)" << endl;
exit( -1 );
}
if ( bCustomNavigation && !bAceFileOnCommandLine ) {
cerr << "Error: If you specify -nav, you must also specify -ace (ace file)" << endl;
exit( -1 );
}
if ( bPrintSingleSignal && !bAceFileOnCommandLine ) {
cerr << "Error: If you specify -singleSignal, you must also specify -ace (ace file)" << endl;
exit( -1 );
}
if ( bMainContigPos && !bAceFileOnCommandLine ) {
cerr << "Error: If you specify -mainContigPos, you must also specify -ace (ace file)" << endl;
exit( -1 );
}
if ( bSolexa2PhdBall && bAceFileOnCommandLine ) {
cerr << "Error: If you specify -solexa2PhdBall, you must not also specify -ace (ace file)" << endl;
exit( -1 );
}
if ( bSelectRegions && !bAceFileOnCommandLine ) {
cerr << "Error: If you specify -selectRegions, you must also specify -ace (ace file)" << endl;
exit( -1 );
}
if ( bAlignments && !bAceFileOnCommandLine ) {
cerr << "Error: If you specify -alignments, you must also specify -ace (ace file)" << endl;
exit( -1 );
}
if ( bPhdBall2Fasta && bAceFileOnCommandLine ) {
cerr << "Error: If you specify -phdBall2Fasta, you must not also specify -ace (ace file)" << endl;
exit( -1 );
}
if ( bFasta && bAceFileOnCommandLine ) {
cerr << "Error: If you specify -fasta, you must not also specify -ace (ace file)" << endl;
exit( -1 );
}
if ( bFastq && bAceFileOnCommandLine ) {
cerr << "Error: If you specify -fastq, you must not also specify -ace (ace file)" << endl;
exit( -1 );
}
if ( bTestReadPhdBall && bAceFileOnCommandLine ) {
cerr << "Error: If you specify -testReadPhdBall, you must not also specify -ace (ace file)" << endl;
exit( -1 );
}
if ( bRemoveReads && !bAceFileOnCommandLine ) {
cerr << "Error: If you specify -removeReads, you must also specify -ace (ace file)" << endl;
exit( -1 );
}
if ( bRemoveContigs && !bAceFileOnCommandLine ) {
cerr << "Error: If you specify -removeContigs, you must also specify -ace (ace file)" << endl;
exit( -1 );
}
if ( bPrintDefaultResources && bAceFileOnCommandLine ) {
cerr << "Error: If you specify -printDefaultResources, you must not also specify -ace (ace file)" << endl;
exit( -1 );
}
if ( bSff2PhdBall && bAceFileOnCommandLine ) {
cerr << "Error: If you specify -sff2PhdBall, you must not also specify -ace (ace file)" << endl;
exit( -1 );
}
if ( bEditConsedrc && bAceFileOnCommandLine ) {
cerr << "Error: If you specify -editConsedrc, you must not also specify -ace (ace file)" << endl;
exit( -1 );
}
if ( bChangeConsensus && !bAceFileOnCommandLine ) {
cerr << "Error: If you specify -changeConsensus, you must also specify -ace (ace file)" << endl;
exit( -1 );
}
if ( bSnpGenome && bAceFileOnCommandLine ) {
cerr << "Error: If you specify -snpGenome, you must not also specify -ace (ace file)" << endl;
exit( -1 );
}
if ( bGenome && bAceFileOnCommandLine ) {
cerr << "Error: If you specify -genome, you must not also specify -ace (ace file)" << endl;
exit( -1 );
}
if ( bValid && bAceFileOnCommandLine ) {
cerr << "Error: If you specify -valid, you must not also specify -ace (ace file)" << endl;
exit( -1 );
}
if ( bDiffChromosomes && bAceFileOnCommandLine ) {
cerr << "Error: If you specify -diffChromosomes, you must not also specify -ace (ace file)" << endl;
exit( -1 );
}
if ( bAddFlowcells && bAceFileOnCommandLine ) {
cerr << "Error: If you specify -addFlowcells, you must not also specify -ace (ace file)" << endl;
exit( -1 );
}
if ( bControlFile && bAceFileOnCommandLine ) {
cerr << "Error: If you specify -controlFile, you must not also specify -ace (ace file)" << endl;
exit( -1 );
}
if ( bFixContigEnds && !bAceFileOnCommandLine ) {
cerr << "Error: If you specify -fixContigEnds, you must also specify -ace (ace file)" << endl;
exit( -1 );
}
if ( bContigEndsFOF && !bAceFileOnCommandLine ) {
cerr << "Error: If you specify -contigEndsFOF, you must also specify -ace (ace file)" << endl;
exit( -1 );
}
if ( bGeneClassifications && bAceFileOnCommandLine ) {
cerr << "Error: If you specify -geneClassifications, you must not also specify -ace (ace file)" << endl;
exit( -1 );
}
if ( bChromosomesFOF && bAceFileOnCommandLine ) {
cerr << "Error: If you specify -chromosomesFOF, you must not also specify -ace (ace file)" << endl;
exit( -1 );
}
if ( bKnownGene && bAceFileOnCommandLine ) {
cerr << "Error: If you specify -knownGene, you must not also specify -ace (ace file)" << endl;
exit( -1 );
}
if ( bPhaster2PhdBall && bAceFileOnCommandLine ) {
cerr << "Error: If you specify -phaster2PhdBall, you must not also specify -ace (ace file)" << endl;
exit( -1 );
}
if ( bPhasterLocations && bAceFileOnCommandLine ) {
cerr << "Error: If you specify -phasterLocations, you must not also specify -ace (ace file)" << endl;
exit( -1 );
}
if ( bPhyloFOF && bAceFileOnCommandLine ) {
cerr << "Error: If you specify -phyloFOF, you must not also specify -ace (ace file)" << endl;
exit( -1 );
}
if ( bMiscProgram && bAceFileOnCommandLine ) {
cerr << "Error: If you specify -miscProgram, you must not also specify -ace (ace file)" << endl;
exit( -1 );
}
// main.cpp_part11 ok to edit since not computer-generated
// get consed resources here
consedResources::getConsedResources( );
setErrorRateFromQuality();
// put consed resources into consedParameters here
new consedParameters( consedResources::pCurrentResources_ );
pAO = stderr;
// printMemory( "memory at startup" );
pCP->filFileOfPhdFiles_ = filFileOfPhdFiles;
pCP->bTerminateAfterStartup_ = bTerminateAfterStartup;
pCP->bReadOnly_ = bReadOnly;
pCP->soCommandLine_ = soCommandLine;
pCP->bAllowTimestampMismatch_ = bAllowTimestampMismatch;
pCP->myTime_ = time( NULL );
pCP->nWhatIsRunning_ = nWhatIsRunning;
pCP->filUserWantsToSaveToThisAceFile_ = filNewAceFile;
// put consed resources into tagTypes here
saveTagTypes( consedResources::pCurrentResources_ );
pCP->postProcessingAfterTagTypes();
// put consed resources into colorDefaults in ctor for GuiApp (below)
// (remove GuiApp completely from autoFinish )
try {
if ( bAutomatedFinishProgram ) {
autoFinish( filAceFileToOpen, nArgc, argv, bContigSpecified, soContig,
soID, bDoExperiments, bJustCheckAutoFinishReads,
soFilenamesFile );
_exit( 0 );
}
else if ( bAddNewReads ) {
addNewReadsAutomated add( filAceFileToOpen, filFileOfReadsOrPhdsToAdd,
filNewAceFile );
add.doIt();
_exit( 0 );
}
else if ( bAutoPCRAmplify ) {
autoPCRAmplify* pAutoPCRAmplify =
new autoPCRAmplify( filAceFileToOpen, filFileOfPrimerRegions );
pAutoPCRAmplify->doIt();
_exit( 0 );
}
else if ( bAutoEdit ) {
autoEdit* pAutoEdit = new autoEdit( filAceFileToOpen,
filNewAceFile );
pAutoEdit->doIt();
_exit( 0 );
}
else if ( bAddAlignedSequence ) {
assert( !filAlignmentFastaFile.isNull() );
if ( filPhdFileWithWRItem.isNull() ) {
cerr << "Error: if -addAlignedSequence is specified, -phdWithWRItem must also be specified" << endl;
_exit( -1 );
}
addAlignedSequence* pAddAlignedSequence =
new addAlignedSequence( filAceFileToOpen,
filNewAceFile,
filAlignmentFastaFile,
filPhdFileWithWRItem );
pAddAlignedSequence->doIt();
_exit( 0 );
}
else if ( bTagSNPs ) {
tagSNPs* pTagSNPs = new tagSNPs( filAceFileToOpen,
filNewAceFile,
filFileOfReadsOrPhdsToAddForTagSNPs );
pTagSNPs->doIt();
_exit( 0 );
}
else if ( bAutoReport ) {
autoReport* pAutoReport = new autoReport( filAceFileToOpen );
pAutoReport->doIt();
_exit( 0 );
}
else if ( bPrintSingleSignal ) {
printSingleSignal* pPrintSingleSignal =
new printSingleSignal( filAceFileToOpen,
soUnpaddedConsPosForSingleSignal );
pPrintSingleSignal->doIt();
_exit( 0 );
}
else if ( bAddReads ) {
addNewReadsWithExistingAlignments add( filAceFileToOpen,
filNewAceFile,
filAddNewReadsAlignmentsFOF,
soChemistry );
add.doIt();
_exit( 0 );
}
else if ( bRemoveContigs ) {
removeContigs myRemoveContigs( filAceFileToOpen,
filNewAceFile,
filContigsToBeRemoved );
myRemoveContigs.doIt();
_exit( 0 );
}
else if ( bRemoveReads ) {
removeReads myRemoveReads( filAceFileToOpen,
filNewAceFile,
filReadsToBeRemoved );
myRemoveReads.doIt();
_exit( 0 );
}
else if ( bPrintDefaultResources ) {
printDefaultResources();
_exit( 0 );
}
else if ( bSolexa2PhdBall ) {
solexa2PhdBall mySolexa2PhdBall( filSolexaFOF, filNewPhdBallFOF );
mySolexa2PhdBall.doIt();
_exit( 0 );
}
else if ( bSelectRegions ) {
addNewReads myAddNewReads( filAceFileToOpen,
filRegionsFile,
filSelectRegionsAlignmentsFOF );
myAddNewReads.doItSelectRegions();
_exit( 0 );
}
else if ( bPhdBall2Fasta ) {
phdBall2Fasta myPhdBall2Fasta( filPhdBall,
filFasta,
filFastq );
myPhdBall2Fasta.doIt();
_exit( 0 );
}
else if ( bTestReadPhdBall ) {
testReadPhdBall testReadPhdBall( filPhdBallForTestRead );
testReadPhdBall.doIt();
_exit( 0 );
}
else if ( bSff2PhdBall ) {
sff2PhdBall mySff2PhdBall( filSffFile, filNewPhdBall, bFOF, filFOF );
mySff2PhdBall.doIt();
_exit( 0 );
}
else if ( bEditConsedrc ) {
guiEditResourcesStandalone myGuiEditResourcesStandalone;
myGuiEditResourcesStandalone.doIt();
_exit( 0 );
}
else if ( bChangeConsensus ) {
batchChangeConsensus myBatchChangeConsensus(
filAceFileToOpen,
filNewAceFile,
filChangeConsensus );
myBatchChangeConsensus.doIt();
_exit( 0 );
}
else if ( bSnpGenome ) {
snpGenome mySnpGenome( filSnps, filGenome, filValidation );
mySnpGenome.doIt();
_exit( 0 );
}
else if ( bDiffChromosomes ) {
diffChromosomes myDiffChromosome( filOtherDirectory );
myDiffChromosome.doIt();
_exit( 0 );
}
else if ( bAddFlowcells ) {
nextPhredPipeline myNextPhredPipeline( filControlFile );
myNextPhredPipeline.addFlowcells( filFlowcellsToAdd );
_exit( 0 );
}
else if ( bFixContigEnds ) {
fixContigEnds myFixContigEnds( filAceFileToOpen,
filNewAceFile,
filContigEndsFOF );
myFixContigEnds.doIt();
_exit( 0 );
}
else if ( bGeneClassifications ) {
geneClassifications myGeneClassifications(
filGenomicLocations,
filChromosomesFOF,
filKnownGene,
filPhyloFOF );
myGeneClassifications.doIt();
_exit( 0 );
}
else if ( bPhaster2PhdBall ) {
phaster2PhdBall myPhaster2PhdBall(
filPhasterFOF,
filPhasterLocations,
filNewPhdBallFOF );
myPhaster2PhdBall.doIt();
_exit( 0 );
}
else if ( bMiscProgram ) {
miscProgram();
_exit( 0 );
}
} // try
catch (ExceptionBase eb) {
cerr << "Fatal consed error: " << eb.szGetDesc() << endl;
cerr.flush();
_exit( EXIT_FAILURE );
}
assert( pCP->nWhatIsRunning_ = nGraphicalConsedIsRunning );
pFILE = stdout;
// create the GuiApp object which contains and manages
// the toplevel widget, display and resource info, etc.
// there is now a global pointer to this sole instance,
// set in the ctor, accessible as GuiApp::pGetGuiApp()
GuiApp guiAppGlobalInstance("consed", nArgc, argv);
// create the ConsEd object, which owns and manages the
// Assembly data structure(s) as well as the lists of
// currently existing ContigWin and Teditor objects.
// there is now a global pointer to this sole instance,
// set in the ctor, accessible as ConsEd::global()
ConsEd* pConsed = new ConsEd();
// I want this after the ConsEd object is created because it uses
// that object.
GuiApp::pGetGuiApp()->startBlinking();
ConsEd::pGetConsEd()->bUsingPhdFiles_ = !bNoPhdFiles;
// ConsEd::pGetConsEd()->bSettingQualityValues_ = false;
// tell the toplevel widget to manage itself
GuiApp::pGetGuiApp()->makeVisible();
if ( pCP->bMakeLightBackgroundInAlignedReadsWindowAndTracesWindow_ )
GuiApp::pGetGuiApp()->changeDefaultToLightBackground();
consedParameters::pGetConsedParameters()->bCreateSocketToControlConsed_ =
bCreateSocketToControlConsed;
if ( bCreateSocketToControlConsed ) {
int nSocketToControlConsedLocalPortNumber;
if ( ! bIsNumericMaybeWithWhitespace(
soSocketToControlConsedLocalPortNumber,
nSocketToControlConsedLocalPortNumber
) ) {
cerr << "Fatal Error: -socket must be followed by a number (the local port number) but instead is followed by " << soSocketToControlConsedLocalPortNumber << endl;
_exit( -1 );
}
pCP->nCreateSocketToControlConsedOnThisLocalPort_ =
nSocketToControlConsedLocalPortNumber;
}
if (ConsEd::pGetConsEd()->bUsingPhdFiles_ )
terminateIfNoPhdDir();
// I want to read the list of libraries before reading the ace file
// to make debugging by the user easier
pCP->pListOfLibraries_ = new listOfLibraries();
pCP->pListOfLibraries_->aLibraries_.soName_ =
"pCP->pListOfLibraries_->aLibraries_ in main.cpp";
pCP->pListOfLibraries_->parseLibraryFile();
maybeTerminateIfAnotherReadWriteConsed();
// consed now takes a command line arg of file to open
if ( bAceFileOnCommandLine ) {
ConsEd::pGetConsEd()->openAssemblyFile( filAceFileToOpen );
// used to pick up basename
ConsEd::pGetConsEd()->pGetGuiTopWindow()->setAssemblyName( filAceFileToOpen.soGetBasename() );
if ( ! consedParameters::pGetConsedParameters()->bErrorMessageDisplayedAtStartup_ )
XRaiseWindow(
XtDisplay( GuiApp::pGetGuiApp()->widGetTopLevel() ),
XtWindow( GuiApp::pGetGuiApp()->widGetTopLevel() )
);
ConsEd::pGetConsEd()->setAssemblyNameOnAllContigwins(
filAceFileToOpen.soGetBasename()
);
ConsEd::pGetConsEd()->perhapsApplyEditHistoryFile( filAceFileToOpen );
perhapsCreateSocketToControlConsed();
ConsEd::pGetConsEd()->updateContigListOnMainConsedWindow();
if ( bCustomNavigation ) {
ConsEd::pGetConsEd()->startUpConsedWithCustomNavigationFile(
filCustomNavigation );
}
else if ( bMainContigPos ) {
ConsEd::pGetConsEd()->startUpConsedAtMainContigPos( soUnpaddedConsPos );
}
}
else {
// popup the file menu for the user to load an
// assembly into this first contigwin
ConsEd::pGetConsEd()->askUserForFileToOpen();
}
readAndProcessReadPrefixFile();
// comment out error handler for making core dumps
// if ( !bEstablishErrorHandler() )
// // try once more
// bEstablishErrorHandler();
if ( bTerminateAfterStartup )
_exit( 0 );
if ( pCP->bAssemblyViewAutomaticallyStartWithConsed_ &&
ConsEd::pGetAssembly() ) {
ConsEd::pGetConsEd()->pAssemblyView_ =
new assemblyView();
ConsEd::pGetConsEd()->pAssemblyView_->createWindow(
ConsEd::pGetAssembly() );
}
printTime( "time for consed to start: " );
// enter the main X application loop, intercepting
// exceptions and retrying
while (true) {
try {
GuiApp::pGetGuiApp()->mainLoop();
}
catch (RWInternalError rwErr) {
GuiApp::popupErrorMessage(
"Gordon C++ class toolkit has thrown an exception: %s",
rwErr.szGetDesc() );
}
catch (ExceptionBase eb) {
if (! eb.bUserNotified()) {
GuiApp::popupErrorMessage("Error (Consed exception): %s",
eb.szGetDesc());
}
}
catch (...) {
GuiApp::popupErrorMessage(
"Error (exception of unknown type)");
}
}
}