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//  Daniel Sommer

//

//  File:  fastq.h

//

//  Last Modified:  April 2011

//

//  Routines to manipulate FASTQ format files





#ifndef  __FASTQ_HH

#define  __FASTQ_HH





#include  "delcher.hh"

#include  "inttypes_AMOS.hh"

#include  <string>

#include  <vector>

#include  <cstring>





const int  DEFAULT_FASTQ_WIDTH = 60;

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



enum FastqQualType {ILLUMINA, SANGER};

const std::string FASTQ_QUALITY_NAMES[] = {"ILLUMINA", "SANGER"};

const uint32_t FASTQ_QUALITY_COUNT = 2;

const FastqQualType FASTQ_DEFAULT_QUALITY_TYPE = SANGER;



bool  Fastq_Read(FILE * fp, std::string & s, std::string & hdr, std::string & q, std::string & qualHdr, FastqQualType qualType = FASTQ_DEFAULT_QUALITY_TYPE);



#endif // #ifndef __FASTQ_HH