tools.h

char* AppendToBasename(char *filename, char *extra);
char *NormalizeSeqName(char *name, int mode);
int ParseArgument(int numargs, char** arglist, char *optionchars, int parse);
int *ParseMultiArgument(int numargs, char** arglist, char *optionchars, int *count);
void PrintNumber(long long int number);
void PrintUnsignedNumber(unsigned int number);
void PrintTime(double timeval);
void PrintProgressBar(double percentage, int lineabove);
void CleanFasta(char *fastafilename);
void ConvertSFF(char *sfffilename);
void ConvertFastaQ(char *fastaqfilename);
void CalculateCoverage(char *positionsfilename, int genomesize);
void ProcessSamFile(char *samfilename, int totalnumreads);
void Process454File(char *rsfilename);
void ProcessMapFile(char *mapfilename, int totalnumreads);
void ProcessSoapFile(char *soapfilename, int totalnumreads);
void fread16be(unsigned short *dest, FILE *file);
void fread32be(unsigned int *dest, FILE *file);