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//  A. L. Delcher

//

//  File:  fasta.h

//

//  Last Modified:  25 November 2002

//

//  Routines to manipulate FASTA format files





#ifndef  __FASTA_HH

#define  __FASTA_HH





#include  "delcher.hh"

#include  <string>

#include  <vector>

#include  <cstring>





const int  DEFAULT_FASTA_WIDTH = 60;

  // Max number of characters to print on a FASTA data line





char  Complement

    (char ch);

void  Fasta_Print

    (FILE * fp, const char * s, const char * hdr = NULL,

     int fasta_width = DEFAULT_FASTA_WIDTH);

void  Fasta_Print_N

    (FILE * fp, const char * s, int n, const char * hdr = NULL,

     int fasta_width = DEFAULT_FASTA_WIDTH);

void  Fasta_Print_Skip

    (FILE * fp, const char * s, const char * skip, const char * hdr = NULL,

     int fasta_width = DEFAULT_FASTA_WIDTH);

bool  Fasta_Qual_Read

    (FILE * fp, std::string & q, std::string & hdr);

bool  Fasta_Read

    (FILE * fp, std::string & s, std::string & hdr);

void  Reverse_Complement

    (char * s);

void  Reverse_Complement

    (std::string & s);

void  Reverse_String

    (char * s);

void  Reverse_String

    (std::string & s);



int  Fasta_Read_String  (FILE *, char * &, long int &, char [], int);





#endif // #ifndef __FASTA_HH