/*
 * PeakSeq
 * Version 1.01
 * Paper by Joel Rozowsky, et. al.
 * Coded in C by Theodore Gibson.
 * io.h
 * This module deals with input/output concerns.
 */


#ifndef IO_H
#define IO_H


//----------------------------------------------------------------------------
// PUBLIC TYPE DECLARATION
//----------------------------------------------------------------------------
/*
 * This type declaration aids in the program's readability.
 */
typedef char* String;


//----------------------------------------------------------------------------
// PUBLIC FUNCTION PROTOTYPES
//----------------------------------------------------------------------------
/*
 * This function converts the string from chr1 to chrM to an integer that
 * 	represents which chromosome it is on.  The X chromosome is stored as
 * 	chromosome 23, Y as 24, and M as 25.  If there is a letter other than X,
 * 	Y, or M, -1 is outputted, denoting failure.
 * cname: the string representation of the chromosome in the format chr#.
 * Outputs the chromosome number, -1 for failure.
 */
int getCnum( const String cname );

/*
 * This function converts a chromosome number to the string chr1 to chrM.  If
 * 	the number is greater than 25, this function returns a NULL pointer,
 * 	denoting failure.
 * cnum: the number of this chromosome.
 * Outputs the string corresponding to this chromosome, NULL for failure.
 */
String getCname( const int cnum );

/*
 * This function moves to the end of the current line before moving to the
 * 	next line in the file.
 * in: the file being read.
 */
void getNewline( FILE* in );


#endif	/* IO_H	*/