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#ifndef _FLASH_READ_H_
#define _FLASH_READ_H_
#include <stddef.h>
/* In-memory representation of a DNA sequence read. */
struct read {
/* The "tag" that identifies the read. */
char *tag;
/* The sequence of the read in ASCII characters (A, C, G, T, N). */
char *seq;
/* The quality scores of the read, scaled to start at 0. */
char *qual;
/* Length of the tag string. */
int tag_len;
/* Length of the sequence string (number of bases in the read). */
int seq_len;
/* Length of the quality string (will be equal to seq_len). */
int qual_len;
/* Allocated sizes of the seq, tag, and qual buffers, respectively. */
size_t seq_bufsz;
size_t tag_bufsz;
size_t qual_bufsz;
};
struct input_stream;
#include <inttypes.h>
extern void
reverse_complement(struct read *r);
extern void
clean_read(struct read *r, int phred_offset, struct input_stream *in,
uint64_t line_no);
extern void
clean_read_for_write(struct read *r, int phred_offset);
extern void
copy_tag(struct read *to, const struct read *from);
extern void
get_combined_tag(const struct read *read_1,
const struct read *read_2,
struct read *combined_read);
#endif /* _FLASH_READ_H_ */
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