C++ CStopWatch::Read方法代码示例

//.........这里部分代码省略.........
		printf("\n%s csv2stats, Version %s\nOptions ---\n", gszProcName,cpszProgVer);
        arg_print_syntax(stdout,argtable,"\n");
        arg_print_glossary(stdout,argtable,"  %-25s %s\n");
		printf("\nNote: Parameters can be entered into a parameter file, one parameter per line.");
		printf("\n      To invoke this parameter file then precede its name with '@'");
		printf("\n      e.g. %s @myparams.txt\n\n",gszProcName);
		exit(1);
        }

    /* special case: '--version' takes precedence error reporting */
if (version->count > 0)
        {
		printf("\n%s Version %s\n",gszProcName,cpszProgVer);
		exit(1);
        }

if (!argerrors)
	{
	if(FileLogLevel->count && !LogFile->count)
		{
		printf("\nError: FileLogLevel '-f%d' specified but no logfile '-F<logfile>'",FileLogLevel->ival[0]);
		exit(1);
		}

	iScreenLogLevel = iFileLogLevel = FileLogLevel->count ? FileLogLevel->ival[0] : eDLInfo;
	if(iFileLogLevel < eDLNone || iFileLogLevel > eDLDebug)
		{
		printf("\nError: FileLogLevel '-l%d' specified outside of range %d..%d",iFileLogLevel,eDLNone,eDLDebug);
		exit(1);
		}
	if(LogFile->count)
		{
		strncpy(szLogFile,LogFile->filename[0],_MAX_PATH);
		szLogFile[_MAX_PATH-1] = '\0';
		}
	else
		{
		iFileLogLevel = eDLNone;
		szLogFile[0] = '\0';
		}

	bSkipFirst = SkipFirst->count ? true : false;

	iMinLength = MinLength->count ? MinLength->ival[0] : cDfltMinLengthRange;
	if(iMinLength < 1 || iMinLength > cMaxLengthRange)
		{
		printf("Error: Mininum element length '-l%d' is not in range 1..%d",iMinLength,cMaxLengthRange);
		exit(1);
		}

	iMaxLength = MaxLength->count ? MaxLength->ival[0] : cMaxLengthRange;
	if(iMaxLength < iMinLength || iMaxLength > cMaxLengthRange)
		{
		printf("Error: Maximum element length '-L%d' is not in range %d..%d",iMaxLength,iMinLength,cMaxLengthRange);
		exit(1);
		}

	strncpy(szInLociFile,InLociFile->filename[0],_MAX_PATH);
	szInLociFile[_MAX_PATH-1] = '\0';
	strncpy(szInSeqFile,InSeqFile->filename[0],_MAX_PATH);
	szInSeqFile[_MAX_PATH-1] = '\0';
	strncpy(szRsltsFile,RsltsFile->filename[0],_MAX_PATH);
	szRsltsFile[_MAX_PATH-1] = '\0';

		// now that command parameters have been parsed then initialise diagnostics log system
	if(!gDiagnostics.Open(szLogFile,(etDiagLevel)iScreenLogLevel,(etDiagLevel)iFileLogLevel,true))
		{
		printf("\nError: Unable to start diagnostics subsystem.");
		if(szLogFile[0] != '\0')
			printf(" Most likely cause is that logfile '%s' can't be opened/created",szLogFile);
		exit(1);
		}
	gDiagnostics.DiagOut(eDLInfo,gszProcName,"Version: %s Processing parameters:",cpszProgVer);

	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Input CSV element loci file: '%s'",szInLociFile);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Input bioseq genome assembly file: '%s'",szInSeqFile);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Output to file: '%s'",szRsltsFile);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"First line contains header: %s",bSkipFirst ? "yes" : "no");
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Minimum element length: %d",iMinLength);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Maximum element length: %d",iMaxLength);

#ifdef _WIN32
	SetPriorityClass(GetCurrentProcess(), BELOW_NORMAL_PRIORITY_CLASS);
#endif
	// processing here...
	Rslt = Process(bSkipFirst,iMinLength,iMaxLength,szInLociFile,szInSeqFile,szRsltsFile);

	gStopWatch.Stop();
	Rslt = Rslt >=0 ? 0 : 1;
	gDiagnostics.DiagOut(eDLInfo,gszProcName,"Exit code: %d Total processing time: %s",Rslt,gStopWatch.Read());
	exit(Rslt);
	}
else
	{
	printf("\n%s csv2stats, Version %s\n",gszProcName,cpszProgVer);
	arg_print_errors(stdout,end,gszProcName);
	arg_print_syntax(stdout,argtable,"\nUse '-h' to view option and parameter usage\n");
	exit(1);
	}
}

//.........这里部分代码省略.........
		}

	gDiagnostics.DiagOut(eDLInfo,gszProcName,"Version: %s",cpszProgVer);

	iMode = Mode->count ? Mode->ival[0] : 0;
	if(iMode < 0 || iMode >= cMaxSupportedModes)
		{
		gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: Unsupported Mode '-m%d' requested",iMode);
		exit(1);
		}

	KMerLen = 0;
	switch(iMode) {
		case 0:					// generate random species fasta sequence
			for(NumInFileSpecs=Idx=0;NumInFileSpecs < cMaxInFileSpecs && Idx < InFiles->count; Idx++)
				{
				pszInFiles[Idx] = NULL;
				if(pszInFiles[NumInFileSpecs] == NULL)
					pszInFiles[NumInFileSpecs] = new char [_MAX_PATH];
				strncpy(pszInFiles[NumInFileSpecs],InFiles->filename[Idx],_MAX_PATH);
				pszInFiles[NumInFileSpecs][_MAX_PATH-1] = '\0';
				CUtility::TrimQuotedWhitespcExtd(pszInFiles[NumInFileSpecs]);
				if(pszInFiles[NumInFileSpecs][0] != '\0')
					NumInFileSpecs++;
				}

			if(!NumInFileSpecs)
				{
				gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: After removal of whitespace, no input file(s) specified with '-i<filespec>' option)\n");
				exit(1);
				}


			KMerLen = kmerlen->count ? kmerlen->ival[0] : cDfltKMerLen;
			if(KMerLen < 1 || KMerLen > cMaxKMerLen)
				{
				gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: K-mer length specified with '-k%d' is outside of range 1..10",KMerLen);
				exit(1);
				}
			

			if(!OutFile->count || OutFile->filename[0][0] == '\0')
				{
				gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: No output fasta file specified with '-o<filename>'");
				exit(1);
				}
			strncpy(szOutputFile,OutFile->filename[0],_MAX_PATH);
			szOutputFile[_MAX_PATH] = '\0';

			if(!RandSeed->count)
				iRandSeed = -1;
			else
				{
				iRandSeed = RandSeed->ival[0];
				if(iRandSeed < 0 || iRandSeed > 32767)
					{
					gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: Random seed specified as '-s%d' must be between 0 and 32767",iRandSeed);
					exit(1);
					}
				}
			break;

		}

	gDiagnostics.DiagOut(eDLInfo,gszProcName,"Processing parameters:");



	switch(iMode) {
		case 0:
			gDiagnostics.DiagOutMsgOnly(eDLInfo,"Mode: 0 (randomise genome K-mers)");
			for(Idx=0; Idx < NumInFileSpecs; Idx++)
				gDiagnostics.DiagOutMsgOnly(eDLInfo,"Use frequency compositions from these genome multifasta file(s) (%d): '%s'",Idx+1,pszInFiles[Idx]);
			gDiagnostics.DiagOutMsgOnly(eDLInfo,"Maintain K-mer composition of length: %d",KMerLen);
			gDiagnostics.DiagOutMsgOnly(eDLInfo,"Genome output file: '%s'",szOutputFile);
			if(iRandSeed >= 0)
				gDiagnostics.DiagOutMsgOnly(eDLInfo,"Random seed: %d",iRandSeed);
			else
				gDiagnostics.DiagOutMsgOnly(eDLInfo,"Random seed: will use current time as seed");
			break;
		}
	
	gStopWatch.Start();
#ifdef _WIN32
	SetPriorityClass(GetCurrentProcess(), BELOW_NORMAL_PRIORITY_CLASS);
#endif
	Rslt = GenerateRandFasta(iMode,KMerLen,NumInFileSpecs,pszInFiles,szOutputFile,iRandSeed);
	Rslt = Rslt >=0 ? 0 : 1;
	gDiagnostics.DiagOut(eDLInfo,gszProcName,"Exit code: %d Total processing time: %s",Rslt,gStopWatch.Read());
	exit(Rslt);
	}
else
	{
	printf("\n%s Kanga randomise genome K-mers, Version %s\n",gszProcName,cpszProgVer);
	arg_print_errors(stdout,end,gszProcName);
	arg_print_syntax(stdout,argtable,"\nUse '-h' to view option and parameter usage\n");
	exit(1);
	}
return 0;
}

//.........这里部分代码省略.........
        arg_print_glossary(stdout,argtable,"  %-25s %s\n");
		printf("\nNote: Parameters can be entered into a parameter file, one parameter per line.");
		printf("\n      To invoke this parameter file then precede its name with '@'");
		printf("\n      e.g. %s @myparams.txt\n",gszProcName);
		printf("\nPlease report any issues regarding usage of %s at https://github.com/csiro-crop-informatics/biokanga/issues\n\n",gszProcName);
		exit(1);
        }

    /* special case: '--version' takes precedence error reporting */
if (version->count > 0)
        {
		printf("\n%s Version %s\n",gszProcName,cpszProgVer);
		exit(1);
        }


if (!argerrors)
	{
	if(FileLogLevel->count && !LogFile->count)
		{
		printf("\nError: FileLogLevel '-f%d' specified but no logfile '-F<logfile>'",FileLogLevel->ival[0]);
		exit(1);
		}

	iScreenLogLevel = iFileLogLevel = FileLogLevel->count ? FileLogLevel->ival[0] : eDLInfo;
	if(iFileLogLevel < eDLNone || iFileLogLevel > eDLDebug)
		{
		printf("\nError: FileLogLevel '-l%d' specified outside of range %d..%d",iFileLogLevel,eDLNone,eDLDebug);
		exit(1);
		}
	
	if(LogFile->count)
		{
		strncpy(szLogFile,LogFile->filename[0],_MAX_PATH);
		szLogFile[_MAX_PATH-1] = '\0';
		}
	else
		{
		iFileLogLevel = eDLNone;
		szLogFile[0] = '\0';
		}




	FMode = (etFMode)(format->count ? format->ival[0] : eFMdefault);
	if(FMode < eFMdefault || FMode >= eFMplaceholder)
		{
		printf("\nError: Requested output format '-M%d' not supported, must be in range %d..%d",FMode,eFMdefault,eFMplaceholder-1);
		exit(1);
		}

	strcpy(szInputFileSpec,InFile->filename[0]);
	strcpy(szOutputFileSpec,OutFile->filename[0]);

			// now that command parameters have been parsed then initialise diagnostics log system
	if(!gDiagnostics.Open(szLogFile,(etDiagLevel)iScreenLogLevel,(etDiagLevel)iFileLogLevel,true))
		{
		printf("\nError: Unable to start diagnostics subsystem.");
		if(szLogFile[0] != '\0')
			printf(" Most likely cause is that logfile '%s' can't be opened/created",szLogFile);
		exit(1);
		}

	gDiagnostics.DiagOut(eDLInfo,gszProcName,"Version: %s Processing parameters:",cpszProgVer);
	const char *pszDescr;
	switch(FMode) {
		case eFMdefault:			// default is for multifasta
			pszDescr = "Multifasta";
			break;
		case eFMcsv:				// CSV entries
			pszDescr = "CSV format";
			break;
		case eFMbed:				// BED entries
			pszDescr = "BED format";
			break;
		case eFMxml:				// XML entries
			pszDescr = "XML format";
			break;
		}
	
	gDiagnostics.DiagOut(eDLInfo,gszProcName,"dump output format: %s",pszDescr);
	gDiagnostics.DiagOut(eDLInfo,gszProcName,"input biosequence file: '%s'",szInputFileSpec);
	gDiagnostics.DiagOut(eDLInfo,gszProcName,"output to file: '%s'",szOutputFileSpec);	
	
	gStopWatch.Start();
	Rslt = Process(szInputFileSpec,szOutputFileSpec,FMode);
	gStopWatch.Stop();
	Rslt = Rslt >=0 ? 0 : 1;
	gDiagnostics.DiagOut(eDLInfo,gszProcName,"Exit code: %d Total processing time: %s",Rslt,gStopWatch.Read());
	exit(Rslt);
	}
else
	{
	printf("\n%s Dump biosequence (generated by genbioseq) file contents, Version %s\n",gszProcName,cpszProgVer);
	arg_print_errors(stdout,end,gszProcName);
	arg_print_syntax(stdout,argtable,"\nUse '-h' to view option and parameter usage\n");
	exit(1);
	}
}

//.........这里部分代码省略.........
		{
		printf("\nSpecified region '-g%d' outside of range 0..%d",Region,eMEG3UTR);
		exit(1);
		}

	NumIncludeChroms = includechroms->count;
	for(Idx=0;Idx < includechroms->count; Idx++)
		{
		LenFileList = (int)strlen(includechroms->sval[Idx]);
		pszIncludeChroms[Idx] = new char [LenFileList+1];
		strcpy(pszIncludeChroms[Idx],includechroms->sval[Idx]);
		TrimQuotes(pszIncludeChroms[Idx]);
		}

	NumExcludeChroms = excludechroms->count;
	for(Idx=0;Idx < excludechroms->count; Idx++)
		{
		LenFileList = (int)strlen(excludechroms->sval[Idx]);
		pszExcludeChroms[Idx] = new char [LenFileList+1];
		strcpy(pszExcludeChroms[Idx],excludechroms->sval[Idx]);
		TrimQuotes(pszExcludeChroms[Idx]);
		}

	if(!infiles->count)
		{
		printf("\nError: No input file(s) specified with with '-i<filespec>' option)");
		exit(1);
		}

	for(NumInFiles=Idx=0;NumInFiles < cMaxNumBedFiles && Idx < infiles->count; Idx++)
		{
		pszInFileSpecs[Idx] = NULL;
		if(pszInFileSpecs[NumInFiles] == NULL)
			pszInFileSpecs[NumInFiles] = new char [_MAX_PATH];
		strncpy(pszInFileSpecs[NumInFiles],infiles->filename[Idx],_MAX_PATH);
		pszInFileSpecs[NumInFiles][_MAX_PATH-1] = '\0';
		CUtility::TrimQuotedWhitespcExtd(pszInFileSpecs[NumInFiles]);
		if(pszInFileSpecs[NumInFiles][0] != '\0')
			NumInFiles++;
		}

	if(!NumInFiles)
		{
		printf("\nError: After removal of whitespace, no input file(s) specified with '-i<filespec>' option)");
		exit(1);
		}

	strncpy(szOutFile,OutFile->filename[0],_MAX_PATH);
	szOutFile[_MAX_PATH-1] = '\0';


			// now that command parameters have been parsed then initialise diagnostics log system
	if(!gDiagnostics.Open(szLogFile,(etDiagLevel)iScreenLogLevel,(etDiagLevel)iFileLogLevel,true))
		{
		printf("\nError: Unable to start diagnostics subsystem.");
		if(szLogFile[0] != '\0')
			printf(" Most likely cause is that logfile '%s' can't be opened/created",szLogFile);
		exit(1);
		}

	gDiagnostics.DiagOut(eDLInfo,gszProcName,"Version: %s Processing parameters:",cpszProgVer);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Processing Mode: %d (%s)",iProcMode,ProcMode2Txt((etProcMode)iProcMode));
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"process for this strand only: '%c'",(char)Strand);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"generated merged features will be at least this length: %d",MinLen);
	if(JoinLen == 0)
		gDiagnostics.DiagOutMsgOnly(eDLInfo,"keep separate features, no merging");
	else
		gDiagnostics.DiagOutMsgOnly(eDLInfo,"merge features separated by upto: %d",JoinLen);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Retain Region: %s",Region2Txt((etBEDRegion)Region));
	for(Idx = 0; Idx < NumIncludeChroms; Idx++)
		gDiagnostics.DiagOutMsgOnly(eDLInfo,"reg expressions defining chroms to include: '%s'",pszIncludeChroms[Idx]);
	for(Idx = 0; Idx < NumExcludeChroms; Idx++)
		gDiagnostics.DiagOutMsgOnly(eDLInfo,"reg expressions defining chroms to exclude: '%s'",pszExcludeChroms[Idx]); 
	for(Idx=0;Idx < NumInFiles; Idx++)
		gDiagnostics.DiagOutMsgOnly(eDLInfo,"merge features from this input BED file (%d): '%s'",Idx+1,pszInFileSpecs[Idx]);		
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Output merged features into BED file: '%s'",szOutFile);

	gStopWatch.Start();
#ifdef _WIN32
	SetPriorityClass(GetCurrentProcess(), BELOW_NORMAL_PRIORITY_CLASS);
#endif	
	Rslt = Process((etProcMode)iProcMode,Strand,MinLen,JoinLen,Region,
			NumIncludeChroms,	// number of chromosome regular expressions to include
			pszIncludeChroms,	// array of include chromosome regular expressions
			NumExcludeChroms,	// number of chromosome expressions to exclude
			pszExcludeChroms,	// array of exclude chromosome regular expressions
		NumInFiles,pszInFileSpecs,szOutFile);
	gStopWatch.Stop();
	Rslt = Rslt >=0 ? 0 : 1;
	gDiagnostics.DiagOut(eDLInfo,gszProcName,"Exit code: %d Total processing time: %s",Rslt,gStopWatch.Read());
	exit(Rslt);
	}
else
	{
	printf("\n%s BED Merge Blocks, Version %s\n",gszProcName,cpszProgVer);
	arg_print_errors(stdout,end,gszProcName);
	arg_print_syntax(stdout,argtable,"\nUse '-h' to view option and parameter usage\n");
	exit(1);
	}
}

//.........这里部分代码省略.........
	if(iMinMergeLength < 0 || iMinMergeLength > cMaxLengthRange)
		{
		printf("Error: Minimum output merged element length '-m%d' is not in range 0..%d",iMinMergeLength,cMaxLengthRange);
		exit(1);
		}

	iMaxMergeLength = MaxMergeLength->count ? MaxMergeLength->ival[0] : cDfltMaxLength;
	if(iMaxMergeLength < iMinMergeLength || iMaxMergeLength > cMaxLengthRange)
		{
		printf("Error: Maximum element length '-M%d' is not in range %d..%d",iMaxMergeLength,iMinMergeLength,cMaxLengthRange);
		exit(1);
		}

	iJoinDistance = JoinDistance->count ? JoinDistance->ival[0] : cDfltJoinOverlap;
	if(iJoinDistance < 0 || iJoinDistance > cMaxJoinOverlap)
		{
		printf("Error: Join separation length '-j%d' is not in range %d..%d",iJoinDistance,0,cMaxJoinOverlap);
		exit(1);
		}

	iRefExtend = RefExtend->count ? RefExtend->ival[0] : 0;
	if(iRefExtend < (-1 * cMaxExtendLength) || iRefExtend > cMaxExtendLength)
		{
		printf("Error: Ref Extension length '-e%d' is not in range %d..%d",iRefExtend,(-1 * cMaxExtendLength),cMaxExtendLength);
		exit(1);
		}

	iRelExtend = RelExtend->count ? RelExtend->ival[0] : 0;
	if(iRelExtend < (-1 * cMaxExtendLength) || iRelExtend > cMaxExtendLength)
		{
		printf("Error: Rel Extension length '-E%d' is not in range %d..%d",iRelExtend,(-1 * cMaxExtendLength),cMaxExtendLength);
		exit(1);
		}


	strncpy(szRefFile,RefFile->filename[0],_MAX_PATH);
	szRefFile[_MAX_PATH-1] = '\0';

	if(RelFile->count)
		{
		strncpy(szRelFile,RelFile->filename[0],_MAX_PATH);
		szRelFile[_MAX_PATH-1] = '\0';
		}
	else
		{
		if(iProcMode == ePMElRefExclusive || iProcMode == ePMElRefRelUnion)
			szRelFile[0] = '\0';
		else
			{
			printf("Error: Rel loci file must be specified in processing mode '-p%d' (%s)",iProcMode,ProcMode2Txt((etProcMode)iProcMode));
			exit(1);
			}
		}

		// now that command parameters have been parsed then initialise diagnostics log system
	if(!gDiagnostics.Open(szLogFile,(etDiagLevel)iScreenLogLevel,(etDiagLevel)iFileLogLevel,true))
		{
		printf("\nError: Unable to start diagnostics subsystem.");
		if(szLogFile[0] != '\0')
			printf(" Most likely cause is that logfile '%s' can't be opened/created",szLogFile);
		exit(1);
		}
	gDiagnostics.DiagOut(eDLInfo,gszProcName,"Version: %s Processing parameters:",cpszProgVer);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Processing Mode: %d (%s)",iProcMode,ProcMode2Txt((etProcMode)iProcMode));
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Reference CSV file: '%s'",szRefFile);
	if(szRelFile[0] != '\0')
		gDiagnostics.DiagOutMsgOnly(eDLInfo,"Relative CSV file: '%s'",szRelFile);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Output processed loci into CSV file: '%s'",szOutLociFile);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Output loci file ref species: '%s'",szRefSpecies);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Output loci file rel species: '%s'",szRelSpecies);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Output loci file element type: '%s'",szElType);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Minimum input element length: %d",iMinLength);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Maximum input element length: %d",iMaxLength);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Ref element flank extension length: %d",iRefExtend);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Rel element flank extension length: %d",iRelExtend);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Merge output elements separated by at most this many bases: %d",iJoinDistance);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Minimum output merged element length: %d",iMinMergeLength);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Maximum output merged element length: %d",iMaxMergeLength);


	// processing here...
	gStopWatch.Start();
#ifdef _WIN32
	SetPriorityClass(GetCurrentProcess(), BELOW_NORMAL_PRIORITY_CLASS);
#endif	
	Rslt = Process((etProcMode)iProcMode,iMinLength,iMaxLength,iRefExtend,iRelExtend,iJoinDistance,iMinMergeLength,iMaxMergeLength,szRefFile,szRelFile,szOutLociFile,
		szRefSpecies,szRelSpecies,szElType);
	gStopWatch.Stop();
	Rslt = Rslt >=0 ? 0 : 1;
	gDiagnostics.DiagOut(eDLInfo,gszProcName,"Exit code: %d Total processing time: %s",Rslt,gStopWatch.Read());
	exit(Rslt);
	}
else
	{
	printf("\n%s CSV Merge Elements, Version %s\n",gszProcName,cpszProgVer);
	arg_print_errors(stdout,end,gszProcName);
	arg_print_syntax(stdout,argtable,"\nUse '-h' to view option and parameter usage\n");
	exit(1);
	}
}

//.........这里部分代码省略.........
		{
		iFileLogLevel = eDLNone;
		szLogFile[0] = '\0';
		}

	iProcMode = ProcMode->count ? ProcMode->ival[0] : eProcModeStandard;
	if(iProcMode < eProcModeStandard || iProcMode > eProcModeScore)
		{
		printf("\nError: Requested processing mode '-x%d' not supported",iProcMode);
		exit(1);
		}

	iMinLen = MinLen->count ? MinLen->ival[0] : 0;
	if(iMinLen < 0)
		{
		printf("\nError: Requested minimum length '-l%d' is negative",iMinLen);
		exit(1);
		}

	iMaxLen = MaxLen->count ? MaxLen->ival[0] : 1000000000;
	if(iMaxLen < iMinLen)
		{
		printf("\nError: Requested maximum ength '-l%d' must be >= minimum %d",iMaxLen,iMinLen);
		exit(1);
		}



	strcpy(szRefFile,RefFile->filename[0]);
	strcpy(szRelFile,RelFile->filename[0]);
	strcpy(szRsltfile,Rsltfile->filename[0]);

	if(FilterRefIDFile->count)
		{
		strncpy(szFilterRefIDFile,FilterRefIDFile->filename[0],sizeof(szFilterRefIDFile));
		szFilterRefIDFile[sizeof(szFilterRefIDFile)-1] = '\0';
		}
	else
		szFilterRefIDFile[0] = '\0';


			// now that command parameters have been parsed then initialise diagnostics log system
	if(!gDiagnostics.Open(szLogFile,(etDiagLevel)iScreenLogLevel,(etDiagLevel)iFileLogLevel,true))
		{
		printf("\nError: Unable to start diagnostics subsystem.");
		if(szLogFile[0] != '\0')
			printf(" Most likely cause is that logfile '%s' can't be opened/created",szLogFile);
		exit(1);
		}

	gDiagnostics.DiagOut(eDLInfo,gszProcName,"Version: %d.%2.2d Processing parameters:",cProgVer/100,cProgVer%100);
	switch(iProcMode) {
		case eProcModeStandard:
			gDiagnostics.DiagOutMsgOnly(eDLInfo,"Processing mode:  Identity = Match/(Match+Mismatch)");
			break;
		case eProcModeIdentity:
			gDiagnostics.DiagOutMsgOnly(eDLInfo,"Processing mode:  Identity = Match/(CoreLength)");
			break;
		case eProcModeAligned:
			gDiagnostics.DiagOutMsgOnly(eDLInfo,"Processing mode:  Aligned = (Match+Mismatch)/CoreLength");
			break;
		case eProcModeScore:
			gDiagnostics.DiagOutMsgOnly(eDLInfo,"Processing mode: score");
			break;
		}

	gDiagnostics.DiagOutMsgOnly(eDLInfo,"reference csv file to process: '%s'",szRefFile);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"relative csv file(s) to processs: '%s'",szRelFile);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"results file to generate: '%s'",szRsltfile);
	if(szFilterRefIDFile[0])
		gDiagnostics.DiagOutMsgOnly(eDLInfo,"Exclude any RefIDs in this filter file: '%s'",szFilterRefIDFile);

	gDiagnostics.DiagOutMsgOnly(eDLInfo,"minimum length: %d",iMinLen);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"maximum length: %d",iMaxLen);

	gStopWatch.Start();
#ifdef _WIN32
	SetPriorityClass(GetCurrentProcess(), BELOW_NORMAL_PRIORITY_CLASS);
#endif
	Rslt = Process((etProcMode)iProcMode,		// processing mode 0: default
					szRefFile,		// reference csv file to process
					szFilterRefIDFile, // exclude any RefIDs in this filter file
					szRelFile,		// relative csv file(s) to processs
					szRsltfile,  	// results file to generate
					iMinLen,		// minimum accepted ref length
					iMaxLen);		// maximum accepted ref length

	gStopWatch.Stop();
	Rslt = Rslt < 0 ? 1 : 0;
	gDiagnostics.DiagOut(eDLInfo,gszProcName,"Exit Code: %d Total processing time: %s",Rslt,gStopWatch.Read());
	exit(Rslt);
	}
else
	{
	arg_print_errors(stdout,end,gszProcName);
	arg_print_syntax(stdout,argtable,"\nend of help\n");
	exit(1);
	}
return 0;
}

//.........这里部分代码省略.........
if (!argerrors)
	{
	if(FileLogLevel->count && !LogFile->count)
		{
		printf("\nError: FileLogLevel '-f%d' specified but no logfile '-F<logfile>\n'",FileLogLevel->ival[0]);
		exit(1);
		}

	iScreenLogLevel = iFileLogLevel = FileLogLevel->count ? FileLogLevel->ival[0] : eDLInfo;
	if(iFileLogLevel < eDLNone || iFileLogLevel > eDLDebug)
		{
		printf("\nError: FileLogLevel '-l%d' specified outside of range %d..%d\n",iFileLogLevel,eDLNone,eDLDebug);
		exit(1);
		}
	
	if(LogFile->count)
		{
		strncpy(szLogFile,LogFile->filename[0],_MAX_PATH);
		szLogFile[_MAX_PATH-1] = '\0';
		}
	else
		{
		iFileLogLevel = eDLNone;
		szLogFile[0] = '\0';
		}

	// now that log parameters have been parsed then initialise diagnostics log system
	if(!gDiagnostics.Open(szLogFile,(etDiagLevel)iScreenLogLevel,(etDiagLevel)iFileLogLevel,true))
		{
		printf("\nError: Unable to start diagnostics subsystem\n");
		if(szLogFile[0] != '\0')
			printf(" Most likely cause is that logfile '%s' can't be opened/created\n",szLogFile);
		exit(1);
		}

	gDiagnostics.DiagOut(eDLInfo,gszProcName,"Version: %s",cpszProgVer);

	PMode = (etPMode)(pmode->count ? pmode->ival[0] : ePMdefault);
	if(PMode < ePMdefault || PMode >= ePMplaceholder)
		{
		gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: Processing mode '-m%d' specified outside of range %d..%d\n",PMode,ePMdefault,(int)ePMplaceholder-1);
		exit(1);
		}

	NumInputFiles = 0;

	for(NumInputFiles=Idx=0;NumInputFiles < cMaxInFileSpecs && Idx < pinputfiles->count; Idx++)
		{
		pszInFastaFile[Idx] = NULL;
		if(pszInFastaFile[NumInputFiles] == NULL)
			pszInFastaFile[NumInputFiles] = new char [_MAX_PATH];
		strncpy(pszInFastaFile[NumInputFiles],pinputfiles->filename[Idx],_MAX_PATH);
		pszInFastaFile[NumInputFiles][_MAX_PATH-1] = '\0';
		CUtility::TrimQuotedWhitespcExtd(pszInFastaFile[NumInputFiles]);
		if(pszInFastaFile[NumInputFiles][0] != '\0')
			NumInputFiles++;
		}

	if(!NumInputFiles)
		{
		gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: After removal of whitespace, no input file(s) specified with '-i<filespec>' option)\n");
		exit(1);
		}

	if(!RsltsFile->count)
		{
		gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: No output BED file specified");
		exit(1);
		}
	strncpy(szRsltsFile,RsltsFile->filename[0],_MAX_PATH);
	szRsltsFile[_MAX_PATH-1] = '\0';

	gDiagnostics.DiagOut(eDLInfo,gszProcName,"Processing parameters:");
	for(Idx=0; Idx < NumInputFiles; Idx++)
		gDiagnostics.DiagOutMsgOnly(eDLInfo,"input fasta sequence files (%d): '%s'",Idx+1,pszInFastaFile[Idx]);

	if(szRsltsFile[0] != '\0')
		gDiagnostics.DiagOutMsgOnly(eDLInfo,"Output to BED file: '%s'",szRsltsFile);

#ifdef _WIN32
	SetPriorityClass(GetCurrentProcess(), BELOW_NORMAL_PRIORITY_CLASS);
#endif
	// processing here...
	gStopWatch.Start();
	Rslt = Process(PMode,NumInputFiles,pszInFastaFile,szRsltsFile);

	gStopWatch.Stop();
	Rslt = Rslt >=0 ? 0 : 1;
	gDiagnostics.DiagOut(eDLInfo,gszProcName,"Exit code: %d Total processing time: %s",Rslt,gStopWatch.Read());
	exit(Rslt);
	}
else
	{
	printf("\n%s Generate BED file from multifasta file, Version %s\n",gszProcName,cpszProgVer);
	arg_print_errors(stdout,end,gszProcName);
	arg_print_syntax(stdout,argtable,"\nUse '-h' to view option and parameter usage\n");
	exit(1);
	}
return 0;
}

//.........这里部分代码省略.........
			{
			gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: After removal of whitespace, no SQLite experiment name specified with '-w<str>' option");
			return(1);
			}
		if(experimentdescr->count)
			{
			strncpy(szExperimentDescr,experimentdescr->sval[0],sizeof(szExperimentDescr)-1);
			szExperimentDescr[sizeof(szExperimentDescr)-1] = '\0';
			CUtility::TrimQuotedWhitespcExtd(szExperimentDescr);
			}
		if(strlen(szExperimentDescr) < 1)
			{
			gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: After removal of whitespace, no SQLite experiment description specified with '-W<str>' option");
			return(1);
			}

		gExperimentID = gSQLiteSummaries.StartExperiment(szSQLiteDatabase,false,true,szExperimentName,szExperimentName,szExperimentDescr);
		if(gExperimentID < 1)
			return(1);
		gProcessID = gSQLiteSummaries.AddProcess((char *)gszProcName,(char *)gszProcName,(char *)szExperimentDescr);
		if(gProcessID < 1)
			return(1);
		gProcessingID = gSQLiteSummaries.StartProcessing(gExperimentID,gProcessID,(char *)cpszProgVer);
		if(gProcessingID < 1)
			return(1);
		gDiagnostics.DiagOut(eDLInfo,gszProcName,"Initialised SQLite database '%s' for results summary collection",szSQLiteDatabase);
		gDiagnostics.DiagOut(eDLInfo,gszProcName,"SQLite database experiment identifier for '%s' is %d",szExperimentName,gExperimentID);
		gDiagnostics.DiagOut(eDLInfo,gszProcName,"SQLite database process identifier for '%s' is %d",(char *)gszProcName,gProcessID);
		gDiagnostics.DiagOut(eDLInfo,gszProcName,"SQLite database processing instance identifier is %d",gProcessingID);
		}
	else
		{
		szSQLiteDatabase[0] = '\0';
		szExperimentDescr[0] = '\0';
		}

	PMode = mode->count ? mode->ival[0] : 0;
	if(PMode < 0 || PMode > 1)
		{
		gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: Processing mode '-m%d' must be in range 0..0",PMode);
		return(1);
		}

	strcpy(szInPE1File,inpe1file->filename[0]);
	CUtility::TrimQuotedWhitespcExtd(szInPE1File);

	strcpy(szInPE2File,inpe2file->filename[0]);
	CUtility::TrimQuotedWhitespcExtd(szInPE2File);

	strcpy(szOutFile,outfile->filename[0]);
	CUtility::TrimQuotedWhitespcExtd(szOutFile);

// show user current resource limits
#ifndef _WIN32
	gDiagnostics.DiagOut(eDLInfo, gszProcName, "Resources: %s",CUtility::ReportResourceLimits());
#endif

	gDiagnostics.DiagOut(eDLInfo,gszProcName,"Processing parameters:");
	const char *pszDescr;
	switch(PMode) {
		case 0:
			pszDescr = "Corelate PE1 and PE2 alignments";
			break;
		}

	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Processing mode is : '%s'",pszDescr);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Experiment name : '%s'",szExperimentName);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Experiment description : '%s'",szExperimentDescr);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"SQLite database file: '%s'",szOutFile);

	gDiagnostics.DiagOutMsgOnly(eDLInfo,"PE1 SAM file: '%s'",szInPE1File);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"PE2 SAM file: '%s'",szInPE2File);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Corelations to file: '%s'",szOutFile);

#ifdef _WIN32
	SetPriorityClass(GetCurrentProcess(), BELOW_NORMAL_PRIORITY_CLASS);
#endif
	gStopWatch.Start();

	Rslt = Process(PMode,szInPE1File,szInPE2File,szOutFile);
	Rslt = Rslt >=0 ? 0 : 1;
	if(gExperimentID > 0)
		{
		if(gProcessingID)
			gSQLiteSummaries.EndProcessing(gProcessingID,Rslt);
		gSQLiteSummaries.EndExperiment(gExperimentID);
		}
	gStopWatch.Stop();
	gDiagnostics.DiagOut(eDLInfo,gszProcName,"Exit code: %d Total processing time: %s",Rslt,gStopWatch.Read());
	exit(Rslt);
	}
else
	{
    printf("\n%s, Version %s\n", gszProcName,cpszProgVer);
	arg_print_errors(stdout,end,gszProcName);
	arg_print_syntax(stdout,argtable,"\nUse '-h' to view option and parameter usage\n");
	exit(1);
	}
return 0;
}

//.........这里部分代码省略.........

	iMode = Mode->count ? Mode->ival[0] : eProcModeStandard;
	if(iMode < eProcModeStandard || iMode > eProcModeStandard)
		{
		printf("\nError: Requested processing mode '-x%d' not supported",iMode);
		exit(1);
		}

	if(RegionsIn->count)
		{
		strcpy(szRegionsIn,RegionsIn->sval[0]);
		TrimQuotes(szRegionsIn);
		if((iRegionsIn = ParseRegions(szRegionsIn)) < 0)
			{
			printf("Error: unable to parse '-r%s' into regions to retain",szRegionsIn);
			exit(1);
			}
		}
	else
		{
		szRegionsIn[0] = '\0';
		iRegionsIn = (cFeatBitIG | cFeatBitUpstream | cFeatBit5UTR | cFeatBitCDS | cFeatBitIntrons | cFeatBit3UTR | cFeatBitDnstream);
		}

	if(RegionsOut->count)
		{
		strcpy(szRegionsOut,RegionsOut->sval[0]);
		TrimQuotes(szRegionsOut);
		if((iRegionsOut = ParseRegions(szRegionsOut)) < 0)
			{
			printf("Error: unable to parse '-R%s' into regions to remove",szRegionsOut);
			exit(1);
			}
		}
	else
		{
		szRegionsOut[0] = '\0';
		iRegionsOut = 0;
		}
	iRegionsIn &= ~iRegionsOut;
	if(!iRegionsIn)
		{
		printf("Error: no regions to retain");
		exit(1);
		}

	iRegLen = RegLen->count ? RegLen->ival[0] : cDfltRegLen;
	if(iRegLen < cMinRegLen)
		{
		printf("\nRegulatory region length '-L%d' less than minimum %d, assuming you meant to use '-L%d'",iRegLen,cMinRegLen,cMinRegLen);
		iRegLen = cMinRegLen;
		}
	else
		{
		if(iRegLen > cMaxRegLen)
			{
			printf("\nRegulatory region length '-L%d' more than maximum %d, assuming you meant to use '-L%d'",iRegLen,cMaxRegLen,cMaxRegLen);
			iRegLen = cMaxRegLen;
			}
		}

	strcpy(szInputFile,InFile->filename[0]);
	strcpy(szOutputFile,OutFile->filename[0]);
	strcpy(szInputBiobedFile,InBedFile->filename[0]);
	strcpy(szInSeqFile,InSeqFile->filename[0]);

		// now that command parameters have been parsed then initialise diagnostics log system
	if(!gDiagnostics.Open(szLogFile,(etDiagLevel)iScreenLogLevel,(etDiagLevel)iFileLogLevel,true))
		{
		printf("\nError: Unable to start diagnostics subsystem.");
		if(szLogFile[0] != '\0')
			printf(" Most likely cause is that logfile '%s' can't be opened/created",szLogFile);
		exit(1);
		}

	gDiagnostics.DiagOut(eDLInfo,gszProcName,"Version: %d.%2.2d Processing parameters:",cProgVer/100,cProgVer%100);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Loci file (.csv) file to process: '%s'",szInputFile);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"bio assembly (.seq) file to process: '%s'",szInSeqFile);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"where to write out fasta with random sequences: '%s'",szOutputFile);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"biobed file containing regional features: '%s'",szInputBiobedFile);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Processing mode: %s",iMode == eProcModeStandard ? "standard" : iMode == eProcModeStandard ? "extended" : "summary");
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Accept random samples in any of these regions: '%s'",Regions2Txt(iRegionsIn));

#ifdef _WIN32
	SetPriorityClass(GetCurrentProcess(), BELOW_NORMAL_PRIORITY_CLASS);
#endif

	Rslt = Process(iMode,iRegionsIn,iRegLen,szInputFile,szInputBiobedFile,szInSeqFile,szOutputFile);
	gStopWatch.Stop();
	Rslt = Rslt < 0 ? 1 : 0;
	gDiagnostics.DiagOut(eDLInfo,gszProcName,"Exit Code: %d Total processing time: %s",Rslt,gStopWatch.Read());
	exit(Rslt);
	}
else
	{
	arg_print_errors(stdout,end,gszProcName);
	arg_print_syntax(stdout,argtable,"\nend of help\n");
	exit(1);
	}
}

//.........这里部分代码省略.........
		{
		gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: No input alignment file(s) specified with with '-I<filespec>' option)");
		exit(1);
		}

	for(NumAlignFiles=Idx=0;NumAlignFiles < cRRMaxInFileSpecs && Idx < alignfiles->count; Idx++)
		{
		pszAlignFiles[Idx] = NULL;
		if(pszAlignFiles[NumAlignFiles] == NULL)
			pszAlignFiles[NumAlignFiles] = new char [_MAX_PATH];
		strncpy(pszAlignFiles[NumAlignFiles],alignfiles->filename[Idx],_MAX_PATH);
		pszAlignFiles[NumAlignFiles][_MAX_PATH-1] = '\0';
		CUtility::TrimQuotedWhitespcExtd(pszAlignFiles[NumAlignFiles]);
		if(pszAlignFiles[NumAlignFiles][0] != '\0')
			NumAlignFiles++;
		}

	if(!NumAlignFiles)
		{
		gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: After removal of whitespace, no input alignment file(s) specified with '-I<filespec>' option");
		exit(1);
		}

	// number of alignment files must be same as the number of SNP files and genome names!
	if(NumAlignFiles != NumSNPFiles && NumAlignFiles != NumRelGenomes)
		{
		gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: Expected same number of genome names, alignment files and SNP files, %d genome names, %d alignment files, %d SNP files",NumRelGenomes,NumAlignFiles,NumSNPFiles);
		exit(1);
		}
	
	MinSpeciesTotCntThres = mincovspecies->count ? mincovspecies->ival[0] : 1;
	if(MinSpeciesTotCntThres < 1 || MinSpeciesTotCntThres > 10000)
		{
		gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: Minimum species total bases '-z%d' must be in range 1..10000",MinSpeciesTotCntThres);
		exit(1);
		}

	MinSpeciesWithCnts = mincovspecies->count ? mincovspecies->ival[0] : 1;
	if(MinSpeciesWithCnts < 1 || MinSpeciesWithCnts > NumAlignFiles)
		{
		gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: Minimum species to call marker '-Z%d' must be in range 1..%d",NumAlignFiles);
		exit(1);
		}

// show user current resource limits
#ifndef _WIN32
	gDiagnostics.DiagOut(eDLInfo, gszProcName, "Resources: %s",CUtility::ReportResourceLimits());
#endif

	gDiagnostics.DiagOut(eDLInfo,gszProcName,"Processing parameters:");
	const char *pszDescr;

	switch(PMode) {
		case ePMdefault:
			pszDescr = "Default marker processing";
			break;
		}

	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Processing mode is : '%s'",pszDescr);

	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Minimum coverage : %d",MinCovBases);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Maximum P-Value : %1.4f'",MaxPValue);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Reference genome assembly name : '%s'",szRefGenome);

	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Minimum total bases for species at SNP call loci : %d",MinSpeciesTotCntThres);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Maximum alternative species coverage at SNP call loci : %d",AltSpeciesMaxCnt);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Minimum number of species with SNP call at same loci : %d",MinSpeciesWithCnts);

	for(Idx=0; Idx < NumRelGenomes; Idx++)
		gDiagnostics.DiagOutMsgOnly(eDLInfo,"Alignments and SNPs from this genome (%d) : '%s'",Idx+1,pszRelGenomes[Idx]);

	for(Idx=0; Idx < NumSNPFiles; Idx++)
		gDiagnostics.DiagOutMsgOnly(eDLInfo,"Input SNP file (%d) : '%s'",Idx+1,pszSNPFiles[Idx]);

	for(Idx=0; Idx < NumAlignFiles; Idx++)
		gDiagnostics.DiagOutMsgOnly(eDLInfo,"Input alignment file (%d) : '%s'",Idx+1,pszAlignFiles[Idx]);

	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Output markers to file : '%s'",szMarkerFile);

	gDiagnostics.DiagOutMsgOnly(eDLInfo,"number of threads : %d",NumThreads);

	#ifdef _WIN32
	SetPriorityClass(GetCurrentProcess(), BELOW_NORMAL_PRIORITY_CLASS);
#endif
	gStopWatch.Start();
	Rslt = Process(PMode,MinCovBases,MaxPValue,MinSpeciesTotCntThres,MinSpeciesWithCnts,AltSpeciesMaxCnt,szRefGenome,NumRelGenomes,pszRelGenomes,NumThreads,NumSNPFiles,pszSNPFiles,NumAlignFiles,pszAlignFiles,szMarkerFile);
	gStopWatch.Stop();
	Rslt = Rslt >=0 ? 0 : 1;
	gDiagnostics.DiagOut(eDLInfo,gszProcName,"Exit code: %d Total processing time: %s",Rslt,gStopWatch.Read());
	exit(Rslt);
	}
else
	{
	printf("\n%s Generate Markers, Version %s\n",gszProcName,cpszProgVer);
	arg_print_errors(stdout,end,gszProcName);
	arg_print_syntax(stdout,argtable,"\nUse '-h' to view option and parameter usage\n");
	exit(1);
	}
return 0;
}

//.........这里部分代码省略.........
		exit(1);
		}

	strncpy(szRsltsFile,rsltsfile->filename[0],_MAX_PATH);
	szRsltsFile[_MAX_PATH-1] = '\0';
	CUtility::TrimQuotedWhitespcExtd(szRsltsFile);
	if(szRsltsFile[0] == '\0')
		{
		printf("\nError: No results file ('-o<file> option') specified after removal of leading/trailing quotes and whitespace");
		exit(1);
		}

	NumIncludeChroms = IncludeChroms->count;
	for(Idx=0;Idx < IncludeChroms->count; Idx++)
		{
		LenChromList = (int)strlen(IncludeChroms->sval[Idx]);
		pszIncludeChroms[Idx] = new char [LenChromList+1];
		strcpy(pszIncludeChroms[Idx],IncludeChroms->sval[Idx]);
		CUtility::TrimQuotes(pszIncludeChroms[Idx]);
		}

	NumExcludeChroms = ExcludeChroms->count;
	for(Idx=0;Idx < ExcludeChroms->count; Idx++)
		{
		LenChromList = (int)strlen(ExcludeChroms->sval[Idx]);
		pszExcludeChroms[Idx] = new char [LenChromList+1];
		strcpy(pszExcludeChroms[Idx],ExcludeChroms->sval[Idx]);
		CUtility::TrimQuotes(pszExcludeChroms[Idx]);
		}

			// now that command parameters have been parsed then initialise diagnostics log system
	if(!gDiagnostics.Open(szLogFile,(etDiagLevel)iScreenLogLevel,(etDiagLevel)iFileLogLevel,true))
		{
		printf("\nError: Unable to start diagnostics subsystem.");
		if(szLogFile[0] != '\0')
			printf(" Most likely cause is that logfile '%s' can't be opened/created",szLogFile);
		exit(1);
		}

	gDiagnostics.DiagOut(eDLInfo,gszProcName,"Version: %d.%2.2d Processing parameters:",cProgVer/100,cProgVer%100);
	const char *pszProcMode;
	switch(PMode) {
		case ePMNDyadRegionDist:
			pszProcMode = "background dyad regional distribution";
			break;

		case ePMNDyadOverlap:
			pszProcMode = "sample dyads overlap onto background dyads";
			break;

		};
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"Processing mode: '%s'",pszProcMode);

	gDiagnostics.DiagOutMsgOnly(eDLInfo,"offset background loci by: %d",BkgDyadOfs);
	if(PMode == ePMNDyadOverlap)
		{
		gDiagnostics.DiagOutMsgOnly(eDLInfo,"offset sample loci by: %d",SmplDyadOfs);
		gDiagnostics.DiagOutMsgOnly(eDLInfo,"window flanking: %d",WindDyad);
		}

	gDiagnostics.DiagOutMsgOnly(eDLInfo,"input background loci file: '%s'",szDyadFile);

	if(PMode == ePMNDyadOverlap)
		gDiagnostics.DiagOutMsgOnly(eDLInfo,"input sample loci file: '%s'",szSampleFile);

	gDiagnostics.DiagOutMsgOnly(eDLInfo,"results file: '%s'",szRsltsFile);

	for(Idx = 0; Idx < NumIncludeChroms; Idx++)
		gDiagnostics.DiagOutMsgOnly(eDLInfo,"reg expressions defining chroms to include: '%s'",pszIncludeChroms[Idx]);
	for(Idx = 0; Idx < NumExcludeChroms; Idx++)
		gDiagnostics.DiagOutMsgOnly(eDLInfo,"reg expressions defining chroms to exclude: '%s'",pszExcludeChroms[Idx]); 

#ifdef _WIN32
	SetPriorityClass(GetCurrentProcess(), BELOW_NORMAL_PRIORITY_CLASS);
#endif
	gStopWatch.Start();
	Rslt = Process(PMode,					// processing mode
					BkgDyadOfs,				// offset background loci by this many bases to derive dyad loci
					SmplDyadOfs,			// offset sample loci by this many bases to derive dyad loci
					WindDyad,				// accept sample dyad as matching background loci if within +/- this many bases
					NumIncludeChroms,
					pszIncludeChroms,
					NumExcludeChroms,
					pszExcludeChroms,
					szDyadFile,				// CSV file containing background dyad loci
					szSampleFile,			// CSV file containing sample dyad loci
					szRsltsFile);			// output results to this file
	gStopWatch.Stop();
	Rslt = Rslt >=0 ? 0 : 1;
	gDiagnostics.DiagOut(eDLInfo,gszProcName,"Exit code: %d Total processing time: %s",Rslt,gStopWatch.Read());
	exit(Rslt);
	}
else
	{
	arg_print_errors(stdout,end,gszProcName);
	arg_print_syntax(stdout,argtable,"\nend of help\n");
	exit(1);
	}
return 0;
}

//.........这里部分代码省略.........
	else
		{
		szInclRegionFile[0] = '\0';
		OfsLoci = 0;
		DeltaLen = 0;
		TruncLength = 0;
		}
	


		// now that command parameters have been parsed then initialise diagnostics log system
	if(!gDiagnostics.Open(szLogFile,(etDiagLevel)iScreenLogLevel,(etDiagLevel)iFileLogLevel,true))
		{
		printf("\nError: Unable to start diagnostics subsystem.");
		if(szLogFile[0] != '\0')
			printf(" Most likely cause is that logfile '%s' can't be opened/created",szLogFile);
		exit(1);
		}

// show user current resource limits
#ifndef _WIN32
	gDiagnostics.DiagOut(eDLInfo, gszProcName, "Resources: %s",CUtility::ReportResourceLimits());
#endif

	gDiagnostics.DiagOut(eDLInfo,gszProcName,"Version: %d.%2.2d Processing parameters:",cProgVer/100,cProgVer%100);
	const char *pszDescr;
	switch(PMode) {
		case ePMdefault:				
			pszDescr = "Default - predict from minor groove";
			break;
		}

	gDiagnostics.DiagOutMsgOnly(eDLInfo,"processing mode is : '%s'",pszDescr);

	switch(FMode) {
		case eFMbedGraphDyads:				
			pszDescr = "UCSC bedGraph dyads";
			break;
		case eFMbedDyads:					
			pszDescr = "UCSC BED dyads";
			break;
		case eFMcsvDyads:					
			pszDescr = "CSV dyads";
			break;
		case eFMbedGraphNucs:					
			pszDescr = "UCSC bedGraph nucleosomes";
			break;
		case eFMbedNucs:					
			pszDescr = "UCSC BED nucleosomes";
			break;
		case eFMcsvNucs:					
			pszDescr = "CSV nucleosomes";
			break;
		case eFMMcsvScores:					
			pszDescr = "CSV dyad scores along genome";
			break;

		}
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"output format is : '%s'",pszDescr);

	gDiagnostics.DiagOutMsgOnly(eDLInfo,"moving average filter width : %d",MovAvgFilter);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"baseline noramlisation width : %d",BaselineFilter);

	gDiagnostics.DiagOutMsgOnly(eDLInfo,"dyad name: '%s'",szTrackTitle);

	gDiagnostics.DiagOutMsgOnly(eDLInfo,"dyad minor groove threshold: %1.4f",Dyadratio);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"dyad immediately flanking minor groove threshold: %1.4f",Dyad2ratio);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"dyad remainder flanking minor groove threshold: %1.4f",Dyad3ratio);

	gDiagnostics.DiagOutMsgOnly(eDLInfo,"input genome file: '%s'",szInGenomeFile);
	gDiagnostics.DiagOutMsgOnly(eDLInfo,"input conformation file: '%s'",szInConfFile);

	gDiagnostics.DiagOutMsgOnly(eDLInfo,"output predicted nucleosomes file: '%s'",szRsltsFile);
	
	if(szInclRegionFile[0] != '0')
		{
		gDiagnostics.DiagOutMsgOnly(eDLInfo,"Offset region start loci by : %d",OfsLoci);
		gDiagnostics.DiagOutMsgOnly(eDLInfo,"Delta region length by : %d",DeltaLen);
		gDiagnostics.DiagOutMsgOnly(eDLInfo,"Truncate region length: %d",TruncLength);
		gDiagnostics.DiagOutMsgOnly(eDLInfo,"include regions file: '%s'",szInclRegionFile);
		}
#ifdef _WIN32
	SetPriorityClass(GetCurrentProcess(), BELOW_NORMAL_PRIORITY_CLASS);
#endif
	gStopWatch.Start();
	Rslt = Process(PMode,FMode,MovAvgFilter,BaselineFilter,szTrackTitle,Dyadratio,Dyad2ratio,Dyad3ratio,szInGenomeFile,szInConfFile,szRsltsFile,
									szInclRegionFile,OfsLoci,DeltaLen,TruncLength);
	gStopWatch.Stop();
	Rslt = Rslt >=0 ? 0 : 1;
	gDiagnostics.DiagOut(eDLInfo,gszProcName,"Exit code: %d Total processing time: %s",Rslt,gStopWatch.Read());
	exit(Rslt);
	}
else
	{
	arg_print_errors(stdout,end,gszProcName);
	arg_print_syntax(stdout,argtable,"\nend of help\n");
	exit(1);
	}
return 0;
}