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#ifndef INCLUDED_ParameterList
#define INCLUDED_ParameterList
/*
* This parameter file is modeifed from SOCS system.
*/
#include "ParseReadsOpts.h"
#include "Flags.h"
#include "ShortReadUtil.h"
#include "ReadsFileParser.h"
#include "stdafx.h"
#include <string>
#include <algorithm>
#include <iostream>
#include <fstream>
#include <limits>
#include <ctype.h>
#include <stdio.h>
#include <stdlib.h>
// Use OpenMP is gcc version is later than 4.2
#ifdef __GNUC__
#ifdef __GNUC_PATCHLEVEL__
#define __GNUC_VERSION__ (__GNUC__ * 10000 \
+ __GNUC_MINOR__ * 100 \
+ __GNUC_PATCHLEVEL__)
#else
#define __GNUC_VERSION__ (__GNUC__ * 10000 \
+ __GNUC_MINOR__ * 100)
# endif
#if __GNUC_VERSION__ >= 40200
#include <omp.h>
#endif
#else
#ifdef _MSC_VER
#if _MSC_VER >= 2000
#include <omp.h>
#endif
#endif
#endif
using namespace std;
class MappingOpts : public CParseReadsOpts
{
public:
MappingOpts(void);
virtual ~MappingOpts(void);
void setDefaults(void);
void clearOutputFileName(bool clear = true);
unsigned int readLength;
unsigned int anchorLength;
string fullCommand;
// I/O options
bool bPrintSamHeader; // Default is true
bool bIgnoreQS; // Default is false
bool bPrintNM; // Default is false
bool bPrintAlignments; // Default is false
bool bPrintAmbigReadsSeparately; // Default is false
bool bPrintUnMappedReads; // Default is false
bool bExcludeAmbiguousReads; // Default is true
bool bPrintAmbiguousReadsOnly; // Default is false
bool bPrintBadReads; // Default is false
bool bPrintFirstAlignmentOnly; // Default is false
bool bGetAllAlignments; // Default is false
bool bMap2ForwardStrandOnly; // Default is false
bool bMap2ReverseStrandOnly; // Default is false
bool bPrintAmbigReadsInOneLine; // Default is false
char logFileN[FILENAME_MAX];
char outputDir[FILENAME_MAX];
char outputFileN[FILENAME_MAX];
char outputFormat[FILENAME_MAX];
char badReadFileN[FILENAME_MAX];
char ambiguousReadFileN[FILENAME_MAX];
char unmappedFileN[FILENAME_MAX];
char readsFileFormat[FILENAME_MAX];
int ambiguousDiffThreshold;
int mismatchScoreThreshold;
int maxAlignPerRead;
int subDiffThreshold;
bool bExcludeAmbiguousPaired;
bool bPrintBestPaired;
bool bPrintRef4PairedInMapping;
bool bPrintPairedRQ;
// The default is output all combinations paired end mappings
bool frOnly; // Paired end can only align to different strand.
bool ffOnly; // Paired end can only align to the same strand.
int disLB; // distance lower bound
int disUB; // distance upper bound
unsigned int truncatedReadPrefix;
char readtag_delimiter;
unsigned int maxThreadNum; // for OpenMp
};
class ParameterList : public MappingOpts
{
public:
ParameterList(void) ;
void setDefaults(void);
bool checkRefValidity(void);
bool truncatReadLength(void);
void getOptsByCheckingExtName(void);
void printSetting(void);
bool validFlag;
// Basic Input
char refFile[FILENAME_MAX];
char indexFileN[FILENAME_MAX];
char seedName[FILENAME_MAX];
string refFormat; // index, fasta, list
int seedId;
// Index
bool bMakeIndex; // Default is false
bool bSaveIndex; // Default is false
// For Pairend Read
bool bMatePairedReads;
char matePairFileN1[FILENAME_MAX];
char matePairFileN2[FILENAME_MAX];
// others
bool bMaskedMathRepeat;
};
bool printOptWarning4PairedEndOpts(ParameterList &P);
bool printOptWarning4PairedEndOpts(ParameterList &P);
ParameterList getParameterList(int argc, const char** argv);
bool retriveReadSetsAndSettings(ParameterList& P, \
vector<string>& readSetsList1,\
vector<string>& readSetsList2);
bool checkReadsSetNamesValidity(vector<string>& readSetsList1,\
vector<string>& readSetsList2);
unsigned int getReadLength(const char* readSetFileName, char expFileFormat = 'N');
bool getReadSetsFilenames(ParameterList &P,\
vector<string>& readSetList1,\
vector<string>& readSetList2);
bool checkFileListIsForPairedReads(const char* readSetListFilename);
bool checkFileListHasTheRightExt(vector<string>& readSetList);
bool withSupportExtFileName(const char* fileName);
bool withFastaExtFileName(const char* fileName);
int selectSeed(ParameterList& P);
void printSynopsis(void);
void printUsageInfo(string helpOpt);
// Overwrite string if the source string is not null
inline bool setStr(char* str1, const char* str2)
{
if (str2[0] != '\0') {
strcpy(str1, str2);
return(true);
} else {
return(false);
}
}
#endif
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